Actually, I think the current recording process is just fine for recording overdubs - what we are lacking is a post-recording process that organizes those notes. At least, that’s my personal workflow: record stuff, then edit it.
Ledger did a script which will sort notes similar to how Renoise does it, but you can call it at any time:
https://forum.renoise.com/t/new-tool-2-8-3-1-reorder-notes-by-pitch/39315
I did a modified version with a different sorting algorithm:
https://forum.renoise.com/t/new-tool-2-8-3-1-reorder-notes-by-pitch/39315
For example, I often prefer matching notes to be located in the same column when recording/programming drums
(imagine something like a hihat - it should occupy just a single column, not be spread all over the place).