Glossary

c/s: crafting per second
CS: Crafting speed (as indicated on info panel when hovering over building)

Q: Why the high overtier machines do not work at full speed as calculated?
A: There is a speed cap from vanilla mechanics, maximum 1 crafting per tick (1/60 second). It is the limit where the "crafting progress bar" (green bar) is filled and considered a finish every tick. These give the speed cap of 60 crafting per second (c/s).
Base time for recipe of iron gear wheel is 0.5 s, it would need a machine at 60×0.5=30 CS to work at full speed. (Therefore, 30 CS is the optimum case.
Without any modules, AM3 +3 (80 CS) will the minimum to run at full speed, or AM3 +2 (20 CS) as the most effective machine for it.
With 4× Speed Module 3, machine CS will increase by 2 times. AM3 +2 (60 CS) is already working at full speed. AM3 +1 (15 CS) will be the most effective machine for it.
With 4× Productivity Module 3, machine CS will drop. AM3 +3 (32 CS) is still the minimum to work at full speed.
If beacon effects are applied, CS rating will change, so the "optimum" overtier may change accordingly. Choose the overtier closest to optimum CS for best production.
Recipe of longer base time will have a higher optimum CS. For example, base time for engine unit is 10 s, optimum CS = 60×10 = 600 CS. So you may need AM3 +4 or even AM3 +5 to work at full speed.

Q: Are effects of Productivity Modules also included in this 60 c/s speed cap as well?
A: This question has to be split into two parts. For the -15% speed malus from Productivity Module 3, it is already included in the CS calculation. See the above FAQ.
For the productivity bonus (+10%) form Productivity Module 3, it counts to a separate crafting progress bar (purple bar), but is still limited to a maximum of 1 finish every tick. Combining the two bars, you can get a maximum of 60+60 = 120 product sets per second.

Q: Can this 60 c/s speed cap be evaded, by other means?
A: In the sense of number of crafting processes, no. But there is a trick: that is to multiply the value of crafting time, ingredients, products by the same factor, and treat it as a new "scaled" recipe. Say, the scaled recipe is using factor of 100. Finishing 1 process of scaled recipe gives the same results of finishing 100 processes of original recipe. Hence, a "slow" speed of 10 c/s of scaled recipe is "equivalent" to 1000 c/s of original recipe! This is how to evade the 60 c/s speed cap.
This idea is fully implemented in Schall Recipe Scaling. Be sure to check it out!

Q: Why the size of high overtiers are not exactly scaling with the number of equivalent machines, say electric furnace +4 being a 48×48 (instead of 15×15 now) entity?
A: Although it would be logical to scale like that, such large entity would generate a large sprite sheet in atlas, and consuming lots of VRAM. This would possible hurt the game performance, which is contradicting the motivation of this mod. To balance between being logical and game performance, the overtiers are now scaled linearly rather than expoenentially in dimensions.

Q: How can I use the high overtiers of heat exchangers or boilers? I can never feed enough water into them!
A: Yes, that was why I limited how high of them can be selected in versions up to 0.17.2.
But I have created a new mod Schall Pipe Scaling in the mean time. With pipes and pumps also available as overtiers, it is now possible to supply that insane amount of fluid flow! To show how to use those overtier pipes, there are some example designs (with blueprints) on its FAQ section.
So new tiers are unlocked in 0.17.3! They are tested to provide their rated performance.

Q: Can you add overtiers of mining drills or pumpjacks as well?
A: No, after some calculations, I found that they will not work (too) well in megabases. Detailed explanation in this post.

Overtiers

Each higher tier is exactly 4 machine of its lower tier, in terms of crafting speed, power consumption/production, pollution, or any other properties.
Number of module slots stay the same as the vanilla machine.

Total amount of raw materials (including number of modules) to craft any overtier machine would be the same as the individual array of vanilla machines. Thus no real benefit or unfair advantage (cheat) in using this mod.
The two advantages are reducing total number of entities, and larger size so more beacons can be applied. These are intentional, since the prime motivation of this mod is to reduce the number of entities and improve UPS for megabases.

It is generally not the best to apply highest overtier to every kind of recipe, because of the crafting speed cap. See the below tables for a quick guideline or detailed formula.

Production Machines

Each production machine has a "crafting speed" rating shown on the info panel. In the following, it would be called "CS" for brevity.

In all the tables below, the listed CS values are Without any modules affecting. You may need to multiply them by the speed modifier if any modules are applied. For example, machine CS is 20 and speed modifier is +200%, the effective CS would be 20 × (1 + 200%) = 60.

Recipe time (RT) is the base time for a crafting, when machine having CS = 1. For example, RT of iron gear wheel is 0.5 s; RT of rocket fuel is 30 s.
The actual crafting speed or crafting rate (called "c/s" in below text) is the CS rating divided by RT value.

c/s = CS / RT

Due to limitation of game mechanics, crafting speed is capped at 1 crafting per tick. This means any machine can never go beyond 60 crafting per second (c/s <= 60).
This limit can be partially evaded by handling the recipes differently, please see the Q&A section
(top of this page).

Assembling Machine 3

The third column shows time of recipes the overtier machine is fully supported without modules. Up to current vanilla game version (0.17.4), the fastest recipes are having 0.5 s (e.g., iron gear wheel). Therefore, AM3 +1 and AM3 +2 do run at full speed for any recipes. AM3 +3 has a minimum recipe time of 1.33 s, therefore it would not be running at rated speed.

Mathematically, AM3 +3 has CS = 80. Iron gear wheel has RT = 0.5 s. c/s = 80 / 0.5 = 160 /s.
But c/s can never be larger than 60 /s, so c/s is still 60 /s.

In vanilla game, longest recipe has RT = 60 s. Therefore, AM3 +6 would be an overkill (indicated by a dagger). You may want to use 3× AM3 +5, or apply speed modules to a single AM3 +5 to achieve the same production rate. Both ways are cheaper than using an AM3 +6.

Chemical Plant

Recipes available chemical plants have quite short RT in vanilla game. For example, CP +4 is already enough for production of battery.

Electric Furnace

Basic vanilla ores (up to 0.17.4) has RT = 3.2 s, so you will only need up to EF +3 to smelt them.

Steel plate has RT = 16 s, so EF +4 would be optimal for it. EF +5 would be an overkill.

Oil Refinery

All available vanilla recipes (up to 0.17.4) have RT = 5 s. Therefore, you can simply apply OR +4 for everything.

Centrifuge

Recipes available to centrifuge all have relatively long time. Nuclear fuel has RT = 90 s, even centrifuge +6 cannot produce at 60 /s! But seriously, do you really need so many nuclear fuel!?

Lab

Lab is handled differently from above machines. It has an orginal CS rating of 1. But for a fully upgraded lab (with lab research speed +250%, as in 0.16.51), CS = 3.5 in vanilla lab. Since this mod is assumed for megabases, here we simply apply the fully upgraded speed.

There are different recipe time (RT) for each tech in current version (0.17.4). They RT ranges from 15s to 60 s. Therefore, a lab +5 would be optimal.

Note

The above text interpretations and conclusions about optimal machines are made for vanilla recipes, but the values in tables are true for any recipes.
Schall Recipe Scaling or some other mods have expanded the RT values greatly. So users should use the values in the tables directly to determine the most suitable machine overtiers.

Power Machines

Note: New tiers are unlocked in 0.17.3, which will need corresponding tiers of pipe system from Schall Pipe Scaling, in order to provide sufficient fluid flow rate to work at full machine speed.

Boiler

Steam Engine

Heat Exchanger

Steam Turbine

Nuclear Reactor

Storage Tank