Rav Hamnuna holds that the exemption of borrowing an animal with it's owner only applies to a case where the owner is borrowed to work in the same melacha as the animal, AND that the owner was there at the time that the accident occurred. This approach in שאלה בבעלים is certainly the most rationale, because the reason for the exemption is that since the owner was there at the time of the accident doing the same work, he should have watched his own animal. This is the approach of the GR"A in aderes eliyahu to explain the concept of שאלה בבעלים. However, the meshech chochma (mishpatim 22:3) points out that this approach doesn't at all work with what we pasken, rejecting rav hamnuna entirely. We hold that שאלה בבעלים is completely dependent on the time that the object was borrowed the owner must have already been working for the borrower (or at least begin immediately), AND it makes no difference if the owner is working with the object that has been borrowed or in something else. What then is the rationale behind this halacha?
The meshech chochma suggests that the rationale is based on a gemara in megillah 26b that says the kedusha of a shul would go away, not only through a sale but even if it is given as a gift because: דאי לא דהוה ליה הנאה מיניה לא הוי יהיב ליה והוי מתנה כזביניה. Here too, it is not common to do such a huge favor for the borrower to lend him an object and work for him at the same time. Therefore, we assume that the owner is only lending and working in exchange for something that he received. Since the owner received something in exchange, the borrower is no longer a borrower but has been downgraded to a renter who is exempt for o'nes.
This approach doesn't explain those who hold that negligence is also patur, and also doesn't explain why he is patur for theft according to those who hold a renter is normally chayev for theft (like a shomer sachar). Perhaps we will have to assume a "lo p'lug" to explain those opinions.
With this we can somewhat explain the gemara's question 96a whether שאלה בבעלים applies when the owner sends his messenger rather than going himself. Does the sending of a messenger also indicate that the owner must have received something significant in return for lending and supplying a worker, or do we only assume that when he himself goes. However, if this is in fact the question of the gemara, it shouldn't really be dependent on the halacha of שלוחו של אדם כמותו anywhere else, it should be an isolated question regarding the assumption in this specific situation. Yet, the gemara compares it to the general din of שלוחו של אדם כמותו by hafaras nedarim.