Fixed the bugs you mentioned in the dev build for the next release. Verified that iVSyncPresentInterval actually works properly in Skyrim Special edition. 1 is for your refresh rate vsync, 2 is for half that, 3 is for a third, and so on. On my 75HZ display, 1 sets it to 75fps, 2 sets it to 37fps, and 3 sets it to 25fps. Not sure how I'll incorporate that. The feature doesn't work properly for the older games, at least for me (Fallout 4 and earlier).
I have this tweak already incorporated into BethINI, but only for Skyrim Special Edition for testing purposes. It is buggy in the current build, as mentioned by GhostGSJ
1. This is merely a default value in case somebody sets the incorrect screen resolution it won't bug out your display. There is a setting in BethINI to fix that ;)
2. Generally speaking, no. However, some mods require specific INI tweaks. BethINI has a list of mods that it recognizes that will automatically detect that need and apply the necessary tweak. However, most mods don't require that. It certainly wouldn't hurt to simply open BethINI and hit Save and Exit just in case.
3. Weapon debris I haven't gotten around to adding, and rain occlusion is impossible to turn off because Bethesda borked that setting, despite the game launcher trying to tell you otherwise.
4. You can make your own changes. BethINI may modify your changes in some cases to improve them (e.g. optimize fade distances for grass and lighting), or remove any that it knows are harmful, or incompatible.
As to iFPSClamp, I have a bug in the current build that could be changing that. Also, iFPSClamp is on the list of controversial tweaks, so make sure you don't tell BethINI to set it to default once you save at the pop-up.
BethINI uses advanced methods for grass, lighting, and other fade distances that cause it to look like that to the game launcher and settings, but that is merely because BethINI is optimizing the distances to show the same amount of grass distance in a way that it will not cause pop-in and decreased performance. No, it is not outdated. It merely is smarter than Bethesda.