So I got this DS3231, unfortunately I've read that using a CR2032 can cause issues since it's not rechargeable and the RTC is meant to charge a battery. But is that only if I power it via 5v? My board has a 3.3v output. would that work?
Who knows, the DS3231 is actually an individual IC, it does not have circuitry to charge a battery.
You probably have an assembled module with a DS3231 on it and a heap of other components. Its the other components, that may or not be fitted, that can be used to charge a battery.
So it depends on which module you have.
If you have the typical eBay DS3231 module, recommended modifications (including defeating the charging circuit) are given here: Using a $1 DS3231 Real-time Clock Module with Arduino | Underwater Arduino Data Loggers
It's a Robojax DS3231
Looks like it's meant for a LIR2032. But it does work with a CR2032. I can't tell if it'll be a fire hazard or not though.
The Amazon listing says it needs a CR2032, but the official site doesn't mention it at all. https://www.amazon.ca/Robojax-DS3231-Precision-Module-Arduino/dp/B07GGM2WZF
Yep, that module is the one covered in the tutorial.
I've read here that you can remove the resistor with the number 201 written on it to deactivate the charging. The article is in german but the picturs demonstrate which component you have to remove.
Bit late but I hope I could help you.