It allows applications that may have updates in the Manjaro repositories or the AUR to update to the newer versions.
Otherwise the old versions in the repository will override octopi’s ability to inform you of the updated version and you would need to already know about them and manually update them yourself.
These are the packages I found had updates after I commented out the blueshell repository:
muon (only because I’m beta testing it)
Note: you can use the Octopi repository editor to perform this operation by simply unticking the radio button and clicking save.
PS: There was an update-pack than includes Frameworks 5.9 (among other things) released today, after I finish testing the update I will post the thread.