Ok I did some more testing, I narrowed the issue down a bit. It's nothing to do with the recipe scaling itself. Weirdness is happening whenever a machine tries to exceed 60 crafts per second.
Quoted from the info on the machine scaling mod:
"This is due to limitation by game engine, only 1 crafting per tick for each machine, or equivalently 60 crafting per second."
"Any high tiers would still have the same output rate, but wasting unneeded power."
This may have been true when you first made the machine scaling mod but it doesn't seem to be true in my testing.
Procedure to reproduce (issue 1):
1. Go to creative/sandbox mode, put down an AM3+2, set the recipe to copper wire. Add 4 stack inserters on one side inputting copper plate from 4 chests (fill them with plate yourself or use bots or infinite chests). Add 9 stack inserters on another side outputting copper wire to 9 more chests.
2. Game reports crafting speed of 20, as per your formulas (c/s = CS / RT), 20/0.5 = 40 crafts/sec. Each craft produces 2 copper wires, 40 x 2 x 60 = 4.8k per minute. Verify the ingame production graph shows 4.8k/min production rate.
3. Add 4x speed module 3 to the machine. Craft speed now 60, crafts/sec should be 120 but game is limited to 60c/s. 60 x 2 x 60 = 7.2k/min which should be the maximum possible with one machine no matter what tier. Observe that the production is indeed 7.2k/min.
4. Now remove the speed 3 modules. Observe that the production does not fall back to 4.8k/min, it stays at 7.2k/min.
5. To return the machine to correct operation set the machine to 'no recipe' and then back to copper wire.
6. The above behaviour occurs if 2 or 3 speed module 3s are added in step 3, but not if only 1 is added. 1 modules brings c/s exactly to the limit, more than one pushes it beyond the limit and triggers this odd behaviour.
With production modules it gets weirder (issue 2).
1. Repeat steps 1 and 2 from above.
2. Put 4x production module 3s in the assembling machine.
3. Place 6 beacons adjacent to the assembling machine, fill all 12 slots with speed module 3s. Crafting speed reported as 68.
4. As before, the limit on production should still be 7.2k/min. I am seeing 14k/min
5. c/s = 68/0.5 = 136. 136 x 2 x 1.4 x 60 = 22848. So less than theoretical output ignoring the crafting limit, but still higher than the limit says it should be.
6. Stranger still, copper plate consumption is at 3.6k/min. With that consumption, maximum copper wire production should be 3600 x 2 x 1.4 = 10080 copper wire per min.
Using an AM3+6 with a large number of stack inserters with 200 capacity I have seen over 1million copper wire per min from a single machine while it consumes only a few thousand copper plate per min. While this is great for UPS, it does feel a bit too cheaty. I've noticed the same with other recipes too, including those in electric furnaces and chemical plants.
The behaviour of issue 2 changes when using scaled recipes. The consumption of recipe ingredients is closer to what it should be (calculated from measured production) depending on the value of the recipe multiplier setting. This is the cause of the discrepancy first noticed with the chemical plants in my opening post.
This whole thing may be a 'bug' in factorio itself (rather than your mods) that has not been noticed because it is impossible for it to manifest with vanilla machines?