Hi,
Thanks for the detailed post and your rationale for the way the token system currently works. My honest thoughts though, personally are that this is way, way overboard for a lot of players, self included.
I'll also state that I don't personally enjoy soulslike levels of difficulty, at all. I like games being challenging, but not to the point where if you make a single mistake you're going to instantly die or be heavily punished for it like can happen at higher levels in this game when you're surrounded on both sides with heavily shielded enemies, snipers taking shots and morters falling.
Considering that each run takes at least a couple hours, and you absolutely must escape to gain tokens, here's what I might personally change.
Damage taken is what immediately springs to mind. Even just at level 8 or 9, 100 or even 200 damage can literally occur just within a second or two of standing still too long, even if all you were doing was placing a bomb. Even if it doesn't count shield damage, 300 damage for 25 percent of your entire score is far, far too little. The same applies to healing, really.
Alternatively, have the score scaling be based off your difficulty, where the current requirements are at the top end for those players that enjoy suffering. lol
The credit, level and kill scaling I think is also a bit steep, but not nearly to the same extent as the damage and healing factors considering the shear number of enemies on screen at a time once you pass level 8.
Speaking of, if the end goal is not only to escape but also take no damage, you may want to scale down enemy numbers a little for what is supposed to be the baseline difficulty.
And while I understand wanting to reward the top end players for doing well, rewards also shouldn't be clamped so tightly that lower skilled players barely get anything for their time and runs. Especially when purchasing all of the upgrades requires something like 300 tokens. I actually did total it up before writing this, but I already forgot how much it actually is.
All this being said though, the game itself is very fun. It's not just a mindless kill everything in sight because you can, you actually need to play somewhat strategically. And I do like that. So while I personally think the progression system needs some rebalancing around the not top end of player skill, props to you on putting out a quality game. And I look forward to seeing what's next.