It's possible Alucard Gets the sword at some point in the game to replace his cross. If we go by the theory that he is Trevor turned Vampire, then perhaps the whip is Holy, and as he progresses he is no longer able to use it, and therefore, switches out?
As for Gabe, his outfit is definitely slightly different. However, It cannot be a flashback, since he has the Wings he got from Carmilla, as indicated by the gold designs on his shoulder armor. The whip he uses is also definitely not the Combat Cross. maybe it's just the lighting, but the chain looks reddish? and it has a morning star tip. And the handle is not a cross.
It's possible that given the game takes place in different eras, that one of those parts of the game is flashback to when Gabriel returned to take over the Vampire Castle. Since he is an expert in the art of the whip, he probably got another one, and set off to take shit over.