Not sure I am understanding your problem.
The current game uses *.3.0.binds - before a particular update (v3?) the game used *.2.0.binds so if you load a 2.0.binds file the game I think saves that as a 3.0.binds file.
If you look inside the file (edit using notepad for example) you will see that the first two lines are:
<?xml version="1.0" encoding="UTF-8" ?>
<Root PresetName="Custom" MajorVersion="3" MinorVersion="0">
Changing the file name does not change the details in line 2 of the file.
I don't use "custom" - I rename binds to give them a descriptive name but I have to also change the Root PresetName in the file too - that is what the game sees and what is listed in the drop-down menu.
Renamed files don't get overwritten by the game in event of an error, only "custom" is overwritten so having renamed files prevents losing your bindings.
I hope that I have not misunderstood and that this is of some help.
P.S. Don't keep copies in the same directory as that can cause issues (changes not being saved etc) because the game goes by what is in line 2, not the file name, so copies have the same line 2 and thus can give issues,