Chiming in weeks late, heigh ho. I coded the little bastards.
Thermal vision does not overlay on top of the welder vision and the welder vision does not prevent eye damage from using welders. Additionally the reason for using thermals is that the vision flag system is BYOND code and implementing an SS13-side sight system for a single questionable use would be pretty unacceptable overhead if the species was played frequently. If someone knows of a cheap and quick way to do per-tick vision updates please let me know because I would love to use it.
The code is not 'snowflakey' if you mean anything remotely close to the proper use of that word, it's entirely generic and integrated into the species system. Any other species could make use of the same mechanics (limb overlay masking would work for tattoos if someone worked on that, for example) if sprites were provided and the proper variables switched over.
Balancing hasn't occurred yet beyond a surface level buff/debuff conceptual pass because the species hasn't gone live. You're complaining about the imbalances of an unstable non-live dev branch. Fix them for your port, sure, but please keep in mind that you're not looking at a finished product.