As far as I know, mods at the bottom of the list are loaded first, which means master files should be at the bottom... But when I run BOSS, it reverses the load order, which means I have to reverse it back manually, which is very tiresome.

Is there a way to change that, or...?

You've got it the wrong way round. Files at the top load first.

Ok, if this is so, fine.

I wonder because several mod authors have advised us to place their files at the bottom, or the top, because "files at the bottom load first".
Or maybe I got everything totally wrong.