I think the key point is that the transfer takes place at the very moment of Shechitah.

Prior to Shechitah, the Korban is still considered the owner's Korban, which is why he performs Semichah. However, as Rashi indicates, once the Shechitah is performed, the animal is no longer regarded as his property. Thus, there is no contradiction. Semichah is done immediately before the point at which the owner's rights cease, whereas our Sugya is discussing the status of the animal from the moment of Shechitah and onward.

From that point onward, the Korban is viewed either as belonging to Gavo'ah or, in the case of Korbanos eaten by Kohanim, as belonging to the Kohanim. In fact, the Gemara itself shortly thereafter explains that certain Korbanos are considered the Kohanim's because they receive them for consumption.

So the owner performs Semichah because, at that moment, it is still his Korban. The discussion in our Sugya concerns the animal's status beginning with the Shechitah itself, at which point that ownership has already come to an end.