I've seen it done several ways, together and separate.
A few examples:
https://sasquatchgames.itch.io/glide (expansion links in description)
https://alexandershen.itch.io/quests-over-coffee (most expansions added (all but Patron) to files)
https://byodinsbeardrpg.itch.io/runecairn (links to expansions broken out)
Oh, and a note of something that's unique to itch.io - when items are added to a bundle, the individual items get discounted but there's no bundle discount for owned items (as opposed to DTRPG where the original items' prices don't change, but owned items prices you paid get deducted from the bundle price.)