There should be a way to avoid this. It gets me everytime I import stems from another DAW and I try to see what is wrong and then remember and bring back all regions to 0 db in inspector. I don't know what is the benefit of this feature.
I had found out that it only happens with Studio One exports and was trying to figure out the reason. It looks like if you check "write tempo to audio" option when you export from Studio One, Logic treats those files like Apple Loops, and do the auto leveling. Turning auto leveling off solved it!