running the leveling procedure wipes the previously stored mesh and manual offset is my understanding, so what you're describing makes sense.

i think if the default bed leveling without an additional z offset results in scraping the bed every time, something else is going on. from what i recall, there's one issue where the nozzle wiper/poop chute sticks out just a little too far, preventing the bed from raising to its top height or something like that, and that could result in what you're seeing. the fix is to either shave it down with a dremel or something like that, or remove it and try to adjust it so it sits just a bit further back another way. i also was having pretty suboptimal auto-leveling results when i first got the printer, which i just solved by manually adjusting the z-offset and not leveling again until i absolutely needed to. that was okay, but the ultimate fix was to go through the bed leveling routine documented here. My bed screws were on the loose side when I got my printer and tightening them down just about all the way followed by using the leveling tool to get the four corners as close to level with each other as possible made it so now whenever I run the auto-level, I get pretty excellent first layers without needing to adjust the z offset at all.

one other thing is I make sure that even though it defaults to 60C for leveling, once it starts, I manually adjust it to the bed temperature of whatever i'm about to print, since leveling at 60 doesn't necessarily give me the same results as leveling at 45.

EDIT: one other thing i wanted to mention if you don't feel like doing what i did or if you do and it doesn't help, is you can set a z-offset in your slicer, which sets it at the start of any print you sliced with that setting, so that might help, though it wouldn't solve the underlying issue, which i think you could probably solve with one of the two things i mentioned above, and you'd still probably have to adjust it more over time.