Bulbapedia says: "Transform changes the user's current type(s), current stats, current stat levels, current move(s), current species, current cry, and current catch rate to that of the target's."
So yes, if you bring out Magikarp against a pokemon that knows transform, the opposing pokemon will get Magikarp's catch rate.
This isn't very useful though, since only Ditto learns Transform naturally. Mew learns it by level up but any time you might encounter one (i.e. an event) it's very unlikely to have Transform.