Yes, this seems to be the likely option. If Gotenks was a Super Saiyan, Buu would only be able to utilize his Super Saiyan power. A transformation not in use is out of reach for Buu.Realistically he should be able to use their SSJ powers. Like, do you think Gotenks stayed SSJ3 inside Boo while he was unconscious? Maybe he magically did but who knows. Boo should just be able to access the full power of anyone he absorbs, but sometimes transformations have weird rules.