Ok, here's what I thought was the most probable explanation for Ichigo's Hollow powers. This is not so much "evidence" for the fact that he got the powers from the pit, but proof that they probably didn't come from Rukia and the Hogyouku.
Hollows are born when one's chain of fate is eaten away (Causing the hole to appear in the chest). We saw this happen with Ichigo in episode 20-something. The chain reaches his body and he is covered by the mask substance. As far as we've been told, this is how Hollows are created and come into existence. If I remember correctly, Urahara and his crew are saying things like "is he becoming a hollow?" Here is another point I brought up earlier:
Note: Shinigami powers are inherent, yet hollow powers are created by reasons stated above. As far as can be told, the Hougyoku separates the boundary between shinigami and hollow. It does NOT create pure hollows. Rather, turns shinigami and Hollows alike into hybrids. So it seems completely illogical to me to say that Ichigo's hollow is a result of this fusion device sealed within someone else.Ichigo got his powers from the pit, because as Zangetsu himself said, Ichigo has his own shinigami powers that Byakuya didn't sense (making Ichigo special regardless of Rukia, possibly due to his being Kaien's reincarnation-or whatever). Byakuya only assumed he had the power Rukia gave him, and took that away. Ichigo was then told to find his own powers among all those boxes. He did so as he was transforming into a hollow, thus his current condition.
I think FrogKing had a good point too:
Now, saying that Rukia gave Ichigo the powers in the initial transfer, you would have to assume that he's had the hollow-powers ever since episode one. Yet nowhere before the pit incident did we see any emergence of any Hollow type activity or powers in Ichigo. It was only after that point that the Hollow became an issue. This is not proof, it just strongly supports theory #1. Even in life-or-death situations, such as his encounter with Byakuya/Renji, he has not used the Hollow powers. One could say he used it to escape the pit (a true life-or-death situation), but remember he was only in that situation BECAUSE he was being turned into a hollow. He escaped by his own means. Quoting myself again:we do know how a hollow is made and curiously [urahara's] test involves the use/discovery of shinigami powers to overcome the transformation. It isn't hard to imagine that his first successful creation involve the (I can't remember what it is called) chain being eatin' then having a strong enough soul to overcome it. Maybe the hougyoku was a 'test-tube' creation and Ichigo was the first 'in vivo' creation (i.e. he was putting the hollow/shinigami creation to a practical situation). Many scientists attempt the same type of experiments: test a model at the bench, then apply the model to a controlled in vivo situation.
Again, nowhere before the pit incident did Ichigo ever show any signs of having a hollow inside of him, or display any Shinigami/Hollow hybrid powers. Going off of Aizen's current (episode 61) explaination, it seems that one is able to surpass a Shinigami's limitations only by becoming a hybrid of Shinigami and Hollow. This would mean that both personalities are being used (such as in Ichigo's fight against Zaraki, and then more pronounced against Byakuya), when the "limit is broken".We know how Ichigo came out of the pit, and it wasn't because of a Hollow, it was because he tapped into his own shinigami powers and was able to escape (though being halfway turned in to a hollow at that point).