My thoughts:
Animation speed: the default never bothered me, so I see no point in adjusting it.
Smooth display: yeah, I absolutely switched that on, since it's off by default for some reason. Take full advantage of the hardware you pay for.
Power button to open menu instead of assistant: I don't even have this setting on GrapheneOS but in general I try to repurpose all the buttons and gestures for something useful, and I don't use the assistant at all. The Power menu would be more useful though if items could be added to it (such as Airplane Mode).
Quick Settings: I absolutely rearrange them since I only find a couple of the tiles useful, and I do use them a lot. It's a major setback that the separate tiles for Wi-Fi and Mobile Data have now been merged into the single Internet. I only keep 8 of them, including Bluetooth, Auto-Rotate, Night Light and Airplane mode and get rid of the rest: this way they fit on a single page.
Also 4. Night Light: I use it with the automatic schedule (dusk till dawn), and find it beneficial. In my experience, the default temperature is too low (making the screen too yellow), so I always adjust it up.
I disable Lift to check phone. I'd also make other adjustments, such as no screen wake on USB power but regrettably GrapheneOS doesn't have a setting for that since it's not an AOSP feature.
Adaptive charging: I disable that too, when I want the phone charged I want it ASAP, regardless of what time of the day it is.
Vibration: I don't use vibration at all.
So, being aware of these settings makes sense but I doubt these are the most important ones. For example, on my phone, you won't even get full screen resolution unless you manually go into the settings and change Screen Resolution to Maximum instead of the default "high." Adjusting this is in my opinion more important than any of the above.
So, to get full advantage of your phone and setup, I'd suggest going through the actual settings one-by-one, even if it takes a little more time.