Hello:
I have been ripping with makemkv since 2011,
with Windows,and later with Ubuntu.
I am setup for triple discs, Pioneer, LG,and Asus.
Based on what I ripped, each going to individual folders e.g 1080p, goes to a 2D folder, uhd goes to uhd area, and recently Dolby Vision goes to specified folder, I just in Ubuntu manually browse to already created folder and rip.
So I would suggest "Ask" at rip time will probably be more flexible regardless of the operating system.
In Ubuntu, the folder icon will show up, to enable you to browse and select.
Thanks.
George