Tosafos raises a contradiction between the gemara in kiddushin which implies that ha'arah does not work as biah for kiddushin, and in yevamos it says that it does work. Tosafos says that if he does only ha'arah then it works, but if he does a g'mar biah then he is only koneh at the completion of the biah since his da'as is on the g'mar biah. The Nemukei Yosef here and Ran in Kiddushin (brought in Beis Shmuel 166:6) writes that by a yevama even if his mind is on g'mar biah, he is already koneh at the time of ha'arah since his intent is not rellevant bec. even if they are both anusim he is koneh her.
However, Tosafos Yeshanim asks How can the gemara discuss whether the positive mitzvah of yibum will push off the issur of a widow to kohen gadol, the issur is violated at the time of ha'arah, yet the mitzvah of yibum is not performed until the g'mar biah, so it is not b'idnah. This question can be answered in many different ways. My point is to focus on the assumption of the question that yevama is only acquired with g'mar biah. It seems to me that the Tosafos Yeshanim understands that since the simple reading of the Torah "lehakim sheim" implies g'mar biah, we assume that a person who does a g'mar biah will have in mind to be koneh only with g'mar biah, and would not be koneh with ha'arah. Clearly, this is against the Ran and Nimukei Yosef, but the question is: Since da'as in not a factor, he should be koneh with ha'arah even if his mind is on g'mar biah (which is the proof of the Ran and Nimukei Yosef)?
Perhaps the chiddush of being koneh even o'nes is limited to a situation where he did not have intent to be koneh. But if he had explicit intent NOT to be koneh his yevama with biah, he would not be koneh her (i am not sure if this is true - any proofs for or against?). Therefore, when he does a g'mar biah the Tosafos Yeshanim understands that it is as if he has explicit intent to be koneh with g'mar biah and NOT ha'arah. That is why they assume that you are not koneh with ha'arah (not like the Ran and Nimukei Yosef).
