Not exactly sure how the WSBK homologation papers work or the designation of factory/reference vs independent team, but.........
Maybe having two "factory" teams allows BMW to take development in multiple directions at the same time. If Bonovo and Rockit are treated as separate factories under the rules, they might be to homologate different racing kits, including separate swingarms, etc. If Bonovo and Rockit are both reference teams, it means Redding will not be detuned based upon Toprak's results or vise versa, not that any detuning is foreseeable for the hapless German team, but you get the gist.
Maybe BMW will literally be running two completely separate factory efforts with different homologations and engine tuning maps and more. If so, I wonder what is stopping other manufacturers. Maybe BMW qualifies under super concessions?