I usually group similar type things into directories so that I don't get much of an extension mix. The exception is my download directory and for that I generally want to order by time or size.
Something like photos processed by darktable are a good example of why this isn’t always practical. You have your raw files and your sidecar files side by side. You could separate them in settings I suspect but that’s not the default and god forbid you ever lose one. If you are in the habit of putting JPEGs in the same place you really want to separate by extension.
I always group by project. The OS can handle different file types in a folder. I need to be able to archive a folder and have all of the files regardless of file types.