I have similar issues around long saving times. It only happens when I'm working with tilemaps. Switching to project folder 'kind of' works, in that not every save is slow after editing a tilemap, though sometimes it will just do a complete slow save for no reason that I can fathom (i.e., I'm not working with tilemaps at all).
I bought an NVMe drive thinking it might be hard drive related, but that had no impact on save times.
I would report this as an issue, but I can't recreate the problem in a standalone project, making me think that this is something that is isolated to larger projects.
Here's a gif of the save time in action. First save is a normal save time, second save shows how long it can take after editing the tilemap.
As you can imagine, this is a pretty big pain in the butt as I'm either having to choose to interrupt my workflow for up to 5 minutes at a time, or go without saving.
imgur.com/a/d1sYnJP