Rather than heal you can just select the clip groups and group them again - it’s just as many keystrokes.
If deselecting “create scene/shot tracks” still causes them to be created, that’s a bug we will fix.
If it’s attempting but failing to do scenes when PT API is disabled - it’s another bug. Will fix.
MB does not pull scene numbers from the burn-ins unless you use the experimental “Split Into Source Clips” feature. If you already have EDLs loaded, MB reads the clipnames of all the stuff in the EDL and tries to work out the scenes.
Note that you can edit the formula used to extract scene numbers - it’s regex 
but LLMs can help.