I don't believe it would affect the power at all as I believe Boo would simply draw that power out of Gotenks once he was absorbed. Comparing the two, we saw Gotenks initially lost a lot of Ki and reverted to base before diffusing, whereas his power remained constant for the whole 30 minutes as Boo, showing the typical rules of Ki in regard to fusing and powering up may not apply for Boo.
For the sake of the thread, however, let's say Boo can only draw out Gotenks' SSJ power. In that case, I believe Gohan would win with high-diff. He'd end up stronger than Boo, though Piccolo's intelligence would allow Boo to avoid being killed by a slip up. However, the fusion time would eventually run out and Gohan would wreck. That is, assuming Boo doesn't hit him with the Super Kamikaze Ghost Attack, as I believe such would be strong enough to either kill or severely weaken Gohan if he takes all of the ghosts head on.