Technically BSL had things that may not have been from SR388, for example the remains of Ridley, Dachoras and the Etacoons.
But many of hte enemies actually originated from Zebes as well. Actually most of the Metroid II managerie do not appear in Fusion. With only a few examples such as Hornoads.
It also had quite a few species from Zebes as well. Bull, Choot, Dessgeega, Geruta, Evirs, Fune, Heat Worms, Gadora, Geemers, Kago, Menu, Namihe, Nova/Sovas, Owtches, Powamp, Puyo, Reo, Rippers, Samus Easter, Scisers, Sidehoppers, Skuletera, Wavers, Zebesians (and all other Space Pirates being held), Zeela are all examples. Zozoro maybe related to the Zeros of Zebes as well.
Of course some of these enemies can also be found on other planets as shown in the Metroid Prime series as well.
But it seems to suggest BSL was likely a space zoo in a way... Possibly collecting species around the galaxy.
Of course the Chozo may have seeded many of the planets around the galaxy with their own bioengineered species anyways... Metroids exist on more planets than SR388, in various degrees of power/mutations... So its all kinda moot...
It's not moot. Fusion was the first game in the series to clearly establish that there were corrupt elements within the Federation hierarchy who were in bed with the pirates, presumably via Faustian deals and whatnot. Other M reintroduced this concept with regard to the re-cloning of Ridley and giving Mother Brain a more compact android body (kinda sorta, not exactly), although it's supposed to take place well before Fusion in the timeline.
Furthermore, as a sort of snob when it comes to the Metroid lore, I have to remind you that the term "Zebesian" is improper and heavily misleading. The "Zebesian pirates" were not natives of Zebes (which I still argue is properly pronounced as "ZEE-biss," as it was commonly pronounced way back in the day, and amateur voice actors and screen actors alike have been in dire need of "Hooked On Phonics" for quite some time now :/ ) but were "processed" genetic experiments. Most, if not all, of the adversaries you face in the original trilogy are products of genetic engineering. The term "Zebesian" comes from Sakamoto being a retard who wasn't paying attention to the lore and improperly decided to retcon Zebes as the pirate homeworld when it wasn't (that would be Urtraghus).
So basically, if Mother Brain has a chunk of the Federation in her pocket, it stands to reason that they'd help re-clone her army and her generals. So, since Fusion unveiled a lot of corruption in the Federation, since such experiments were - according to the games - illegal, and the Feddies shouldn't have anything like the BSL, that's the reason for the mix of Metroid II and Super Metroid critters.