How do you deal with Facebook over-attributing conversions?

If you are using FB SDK, it's probably just FB attributing conversions that Appsflyer attributed to other ad networks, just because FB doesn't know about this. So if you want to ensure your adsets get the full picture for hopefully better optimization, you want to keep it this way (since what matter is actual user behaviour and other channels are just unnecessary noise in this). You can still using Appsflyer (and/or your product analytics tool) for accurate reporting. 

If this is still stil important for you for some other reason, you can remove FB SDK and just forward all events to Ads Manager through Appsflyer. In that case you'll have a 100% match, but Facebook will basically get less data which will supposedly affect the optimizaiton. "Supposedly" because we don't really know, but it's just common sense

It's likely that ad networks have different install counts from attribution partners. After all, that's the whole point of attribution.

Just make sure you understand how attribution is modeled and done (and agree with that methodology) then use that as the source of truth. You can use what the ad networks report as "installs", but this is mostly just a double check. I've seen some companies be ok with +/- 20% and do really well with UA. Dialing into making ad network installs match your attributed installs just means you're agreeing with a methodology the ad networks like. Obviously if that's what you want go for it, but you should use the attribution model that works best for your business.

You can either change your attribution window on Facebook or with the other networks that you are running ads with. The SANs get first dibs at attribution, but they (and especially Facebook) tend to drive the best and most traffic, so it usually doesn't make sense to be more restricted with attribution windows on them.