Would it be possible to allow for negative bonuses? For instance making quality machines much faster but consume much more power, have a higher science pack drain, consume more resources, have a smaller mining area etc.

Also some modded labs use custom quality science pack drain, the use Quality Drain modifier setting currently will overwrite the custom drain %.

To answer the first question, most of the ranges provided are already within the allowed limits the prototype provides. I am not sure I could do what your suggesting without making custom entities, which is not something I intend to do with this mod. (most of these values are required to be positive)
Edit: I looked at energy usage, and it does not say it is limited to 1 (going above 1 would increase energy costs), so I would have to test if its possible, but it may be.

As for the second topic regarding science pack drain, there are two settings that exist on labs. science_pack_drain_rate_percent (int) and uses_quality_drain_modifier (boolean). We do not touch the science_pack_drain_rate_percent on the labs itself (such as biolabs having 50%) and only mark the value of uses_quality_drain_modifier as true or false. If the addon in question is modifying the quality prototype drain % then we would have an overlap.

What is the mod your are referring to? The best solution I can think of would be checking for the setting "quality affects lab drain" to be true before making the adjustments to the quality prototype drain % and not setting anything on the lab prototype if its false (since that is default). Then the mod could add its own entities which will have the property set to true and modify the global quality prototype drain % on its own. But you would also lose the ability to enable the setting, since it would overlap their implementation.

I looked at it some more, and a few things could be adjusted to allow for higher energy use when gaining quality:
Asteroid Collectors
Crafting machines (includes furnaces if enabled)
Beacons

Currently its getting late and I try not to make releases before going to sleep. I will come back to this soon and look at what else could be adjusted like this to give a penalty for gaining quality.

Note: The adjustment to changing resource cost for crafts is not something that is available in the protoype options. The other suggestion of having higher science pack drain is also not possible, as its limited to a value between 0 and 1. Also mining drill radius bonus must be above 0. So those are a non starter, but would be interested in hearing what else you might think are worth exploring.

to test some of this stuff before heading to bed, ended up with this funny result when adjusting the asteroid collector below 0. It makes the collector function without power sources. :P I think I will keep the limit of 0 for the minimum, but allow it to go up to 10 now.
I also tested furnaces and crafting machines, and allowing the reduction to go negative works to increase the energy cost with quality levels.

It looks like the energy usage is the only really applicable change, unless you have other ideas than the ones mentioned. I should have a push for this tomorrow sometime later in the evening. Most of the actual edits are completed, just have to also modify the tooltips to explain the possible modifications.

For the lab I am specifically talking about the cryo lab from muluna
Would it not be possible to check science_pack_drain_multiplier &| uses_quality_drain_modifier and not change the settings if either are true? or at least using the current value in the calculation?
I wasn't sure on the other stats, I would assume you could make the bonuses for higher quality prototypes negative by making the base prototype have the minimum possible stats and upgrading the normal quality to the original settings but that would likely be annoying to do per input and might have some unintended side effects. I was mostly just curious on if the ranges were limited by the game or not.
If the normal quality science_pack_drain_multiplier was editable that should allow negative scaling for science pack drain

If beacons can be changed that would be most of what I was hoping for, it was my primary reason for wanting negative scaling, I feel like for low power environments quality beacons are so overpoweringly good

The issue is that science_pack_drain_multiplier is an option on the quality prototype itself. This affects all labs which have uses_quality_drain_modifier set to true.
Allowing their implementation to take the wheel and modify the values is the only real option in this case, since we cannot have different values for the global setting.

That mod does have the option of doing per quality modifications to their labs, its kinda hacky since you need to replace the entity with its quality variant. But then they would be able to set each lab of various quality's science_pack_drain_rate_percent so that both adjustments could co-exist. I tend to not like entity replacement implementations, since it causes other issues. But it is an option, although quite an ask for the developer behind that. It would also introduce double scaling for their labs if you enable quality scaling through this mod, so I am not even sure if that's something they really want to do.

I guess the final suggestion that would be more reasonable, would be to have them change that science_pack_drain_rate_percent on their lab proto across all qualities. Then they can decide if it should be more powerful than biolab or not (biolab is 50%). Then the two mods would co-exist without needing any fancy footwork.

ok, after looking at their code, their cryolab is a duplicate of the biolab. So it gains the inherent drain percentage of 50%.
They commented out an adjustment to the drain % which would have put it to 45%, and probably opted to instead implement their 10% reduction per quality level. I am not sure if they really would want to do the suggestions I made, since it seems they have already considered them. Now I feel fairly confident that the change I made would best fit the situation. Enable the modifications in this mod, and overwrite theirs, or disable the adjustments here and let them do them for just cryolab. (since they want them to be the endgame solution, that would be fitting to let them apply it to only those labs)

the proposed changes are now in the latest release.