Don't know if you found a solution but I did. Here's what you do:
im my case I save a lot. Like, I save after every operation. This causes Logic to keep lots of saved audio files in the project that I've overwritten a dozen times already. I might perform 20 takes of a passage in a song I have. Logic will keep all 20 takes even though I've deleted the audio file in the editor window. This causes my 3 min song to bloat out to 2-3GB in size.
When I'm reasonably sure I like the condition of my song and it's structure I will then do the following:
Save a new version of the project. Then open "window - project audio". This opens the project audio window. In this window I select "edit - select unused audio". This highlights all the audio files that have been deleted/overwritten by myself during my recording and editing. I then hit the Delete key. I believe Logic then confirms the delete command and deletes the unused audio. I close the window and save a new copy of the project. Now my file size is a sane number (450mb for example) rather than the 2.5GB it was before. Of course doing this I've eliminated the ability to "undo" any audio editing/deleting but I've already confirmed that fact.
Hope this helps you out. It helped reduce a 6 min project that was 5.7GB back to a sane number of 890mb. I guess you can say I do a lot of, umm, takes