Yes you are correct, KOTORModSync and the default instructions file are capable of following the mod build exactly. If you uncheck or check a mod from the list, any instruction you'll see on the mod build post is respected and followed. See https://pastebin.com/7gML3zCJ for more information on how KMS handles this internally.
for example, if you have the mod `HD Visas Marr` selected for install, you might remember the modbuild says that 3 specific files must be deleted for the ultimate character overhaul patches. This is how we handle that instruction:
So yes, simply select the mods you want to install from the left list, press install, and let KMS worry about how to handle it all.