Nick has a good point; Apple is definitely going out of its way to make things difficult for people who want to do their own repairs or even those who want a repair that doesn't cost as much as what Apple charges.
I haven't heard anything about battery percentages not working on any phones up to this point, but honestly, it wouldn't surprise me.
To be honest I'm an Android guy so I'm not up on all of the Apple update information, but my first thought would be that you should roll back your iOS version to 16.x and see if your percentage comes back. I'm afraid I can't help telling you how to do that though.
You mentioned an iFixit battery; I assume that means you replaced your own battery, right? And went through the Important Battery Message pop-ups and the loss of the battery health information, right?
Just to clarify, as of the iPhone XS, Apple started pairing the battery to the logic board, which results in the "genuine" battery message if an unpaired battery is used, and of course only Apple can do that pairing. Current battery repair dictates that you have to keep the existing BMS circuit off the original battery and just replace the bare cell. If that wasn't bad enough, then with the iPhone 11, they changed the way the battery health information is stored and made it impossible for the existing programming devices to clear the health percentage to 100% and the cycle count to zero. That means after the 11, even if you reuse the BMS you'll be stuck with the old health values.
So yeah, since you now have an unpaired battery it is entirely possible that iOS 17 is penalizing you for not having a paired battery. As I mentioned, the only way to verify that would be to roll back to a previous 16.x version and see if it goes back to working. I know I personally would be very interested in finding out if that's the case, so let us know if you're able to do that roll-back and what happens when you do.