If a story has Celeste and her curse present, it’s a BA universe story.
All other stories, such as Bigfoot’s a Hoax, The Comeback Kid, Reversal of Fate… these are all written in the canon Supernatural universe with only small tweaks to the storyline, mostly in the style of a case!fic.
Dean is cursed to be tiny in Brothers Kept, the lucky duck, so it takes place in an admittedly-twisted version of the BA universe.
Meanwhile, Jacob’s size change was due to chaos spellwork when he was a giant, and the person that is responsible for his current ‘little’ issue the story ended on has yet to be revealed, and will be a big part of the sequel (which we currently only have the description written down for).
There are a few storylines that will be in the Brothers Apart multiverse yet have both brothers be full-sized (Brothers United, Brothers Chosen). We know it’s the same multiverse because there is a curse victim in the story (Oscar, Stan Baker).
Hope this helps!