If you go commenting out classes manually then there is no official guarantee your export will work. The way it's supposed to be done is, you disable modules in your SCons command (and of course have the export templates built yourself too). If the doc don't show how to turn off 2D physics you might need to do a request for it to be supported.
I don't think server APIs are supposed to be removed, what usually happens is, they get replaced with a dummy version that does nothing, because otherwise you would have to go through the tedious task of commenting out all calls to them through the codebase. That's quite bad if you want to sync up with upstream Godot afterwards. But again, if you want this officially, better go ask for the feature (or PR it, if you can get it to work).
Physics Frame Time is about 0.01666
That precise value really looks like a report of
delta time, not the actual time physics takes to process. Physics should have zero impact on CPU if you don't use any.