I fixed this issue by deleting all profiles for my phone from MMW and starting over.

And suddenly, the issue is back.

MMA appears to think my internal memory and my sdcard are one and the same.

Yesterday's MMW update seems to have fixed whatever the issue was.

Logs uploaded, 3V0TCUASJW

I'll try when I get home tonight.

Could you please send me the log after you change the settings for one storage. Please go to About dialog->Send logs and post your log ID here.

I have LG G4 too and I cannot replicate it.

I'm using MMA 1.2.0.0587 and when I make a change on my external storage, it makes the same change on internal. For example: I don't want to use my internal storage for syncing, however, when I deselect the internal storage, it deselects the sd card too. When I reenable the sd card, internal is reenabled.
LG G4, Marshmallow.

I would submit a ticket, but my support account is still messed up.