I have tried myself quite a bit on mathecatically describing balance. I am currently at the stage: Complex system even just for direct fire units you will only get to a precision of 10% of the balance mass cost at best. There are so many unit stats that change the strenght of a unit. Easiest to start is with effecitve DPS, HP and Masscost. But then you have a lot more stats like energy cost, movementspeed, range!!, firecycle (regarding alpha damage and overkill, which also quite depends on the army composotion you are facing.), turret turn speed, hitbox size, acceleration. And I am sure there are at least twice more stats than I have named here that effect balance. So a theoretical approach via those unit stats becomes very hard to do. It can be usefull when you have to first set a baseline for balance for a mod etc. I did help Dragun with his SCTA mod a bit with this and an efficiency calculation based on lanchesters laws. But that is only a base line after that you can only improve balance via playtesting.
I am going to talk about the medusa bomber stun issue as an example. I find it quite hard to compare the stun of a medusa and the bomber. Mostly because one is an air unit and one is a land unit. So the counters to each other are quite different. Also the bombers main advantage is that it is very fast and is not restricted by terrain. So it needs to be less efficient than a medusa because it can attack way behind the front line whereas the medusa is not capable of doing so. The stun is rather a gimmick for later game use of the bomber because it is cheap and can stun high tier units. Also medusa usually gets dodged, whereas t1 bombers attacking an army usually don't get dodged.
But the biggest issue in my opinion is that you are asuming all tiers of all domains of all factions should be equally strong. That is not the case and is not desired as far as I am concerned. Quite similar balance is required because of the map diversity present in FAF. Some domains have a huge advantage over other on some maps. This results in very similar factions if you want to have interesting games between all factions on all maps. But you still have a bit of wiggle room and in my opinion it should be used. So that is the reason there isn't even an intent to make all t1 bombers equally strong (even if it was possible). They need to be comparable but I am quite certain if you made a statistial analysis of all replays and just calculate the average vet of all t1 bombers in all games it would not converge towards the same value for all bombers. And quite often you don't even have an equivalent unit in the other faction.
Balance is messy and as far as I can tell it is currently done by a couple of the top players having a discussion about their intuition of what is op and what is not. Another problem on top of that is balance is distorted on what tactic (unit composition etc.) currently is in fashion. Also ease of use has a huge impact. Most memorable example that comes to my mind is the introduction of SCAU presets.
If you are interested this is the (old) combat efficiency of selected units calculated via a partial discretization of lanchesters laws wich only takes HP, Mass and avrg DPS into account: