It does seem very likely that Gearbox took SEGA's initial $60,000,000 investment and allocated a good number of their personnel and probably a good portion of those funds to Borderlands and Borderlands 2 instead, according to insider reports from both lowly QC testers as well as now an anonymous (but confirmed) developer.
Pretty sad stuff from Gearbox. It's great that they found their one trick with Borderlands, but between Duke Nukem Forever and now Aliens: Colonial Marines I have to wonder if the gaming community might not be better off were this company to go under in lieu of a potential lawsuit coming from SEGA. Regardless thereof, there will certainly be a community backlash to deal with.
Personally, I won't buy a Borderlands 3 knowing that there is a good chance the franchise was founded on the deception of a separate publisher, even though I'm not an Aliens: Colonial Marines owner myself. It's just the principle of the matter.