Did a quick check through my mod list (There is quite a few I have installed) but miniloaders is the only loader mod I have installed, and I don't see any other mods that would have any obvious effect on structure orientation.
Here's a list of all the mods I have active, as well as (Tags) for what each mod is. https://justpaste.it/9f2ku
This is the best I could capture within 7 seconds of automatic readjustment with snapping disabled.
https://i.gyazo.com/1a9831e49a1dd3dfd22b6dd29968c851.mp4
This occurs regardless if the belt is in line with the miniloader or perpendicular, and occurs with splitters and Underground Belts as well.
UPDATE: I've disabled all of my mods except Miniloaders to test. They still automatically re-orient when a belt-type object is placed in front of or behind them. I enabled and disabled snapping to make sure it wasn't just a glitched setting save or something as well. Also I'm running on version 0.17.79, if that makes a difference.
Also, to clarify regarding the hotkey, I said I'd like a hotkey for rotating the structure, since R only swaps the flow direction. That's not to say that snapping toggle as a hotkey isn't a good idea too though.
Perhaps swap the functionality, have R rotate the structure as normal, and have flipping the flow be Ctrl+R, in line with changing input rotation for Bob's Inserters?
UPDATE 2: I've made the jump to 0.18, most recent version. The behavior still remains the same, even with it being the only mod active.
UPDATE 3: Seems there's actually a setting in-game in the 'Other' options section called "Use different mod settings per save"
Disabling it should allow miniloader snapping to remain unticked between new games, meaning you wont have to mess with where the setting is. :)