This is how Bash an import works. Import is a function which will transfer the specific import data (i.e. NPC Faces, Graphics, Stats, etc) while disregarding load order, except with other similar imports (i.e. import stats gives the mod priority over all stats unless there is another mod with import stats present). When you leave a mod checked before you rebuilding your Bashed Patch, you are telling Bash to only import the data when it will resolve a conflict.
Example: LtbD changes all cells' light and Mod X changes one cell's ownership. Mod X load later so without Bash you wouldn't get the lighting in the one cell that Mod X is changing owners. Now say you tag LtbD with C.Light but leave it check, Bash will combine the changes for that one cell Mod X edits so that it has LtbD light and Mod X ownership. Now say you tag LtbD with C.Light and leave it unchecked before rebuilding your Bashed Patch. Now Bash will again combine the ownership and light edits for the one aforementioned cell but it will also import every single cell light edit that LtbD makes because the mod is unchecked.
If you still have further questions, feel free to PM me. I know my explanations are never that great even though they make sense in my mind
