From memory the join tool sorts by file name but it would be fairly straight forward to add manual sorting as you suggest.
I envisioned this would be used to join album tracks into a single FLAC and therefore the files would already be numbered (in track running order).
Yep, my files always just have the title without track number in the title so it would be helpful to have a "#" column to sort by using the tags. The workaround I've used is to add the files one by one which is a bit cumbersome for albums with lots of tracks. One other thing I noticed once is when I joined a lot of tracks at one time there was an error with the resulting file and so I ended up joining the tracks in smaller groups which was fine. I didn't look into it further so not sure if it really was because of the number of tracks joined together.