This may seem like a dumb question but I have an inkling of bear knowledge on how electronics can work. I know when wires don't make direct contact with each other they can burn the air so to speak and plastic near the contacts. So my question is by running a device next to 0% battery can there be even a small possibility that it can hurt a device?. I asked this because I don't trust the controllers to tell me the exact percentage of battery power left. I've been running on 10% for a while and the controller seems fine.
Not sure if this helps or even relates to your question but, I have been using the KeenPower usb rechargable AA's that are 1.5v @ 1200mah. These are the ones that you remove the end cap and plug them straight into usb to charge. They charge quickly, last an ok amount of time, and more importantly they are sustainable. So I'm not chunking batteries in the trash every other day.
The problem with this battery I think fits you questions because the quest 2 will report them as 100% until they are dead. So basically they are giving 100% power until empty in which case they simply turn off.....no warning! You'll be playing beat saber and suddenly you'll get to watch as your saber floats off into the void. But at only $11 for 4 rechargable aa's on amazon, its fine because that covers 2 sets of controllers(I have 7 quest 2's) and it only takes 30-45 to recharge them. Ive been using them since Jan and haven't noticed any issues with the controllers because of using them till they are dead. I believe that I'm ok qualified enough to say that seeing as that is data based off of having 14 controllers being used this way on a daily bases since Jan lol. Now that being said, use your own judgement because I can't forsee the future contrary to what my kids think lol so they could all burst into flames any second now, who knows!