In my opinion, a joint agreement of boundaries of a soon to be annexed country would be beneficial to both parties.

This is a rough analogy that doesn't touch on many of the intricacies of global politics so bear with me. If you and your neighbor both have a claim to a plot of land between you, and your options are to work together and come to an agreement, or to fight over it, wouldn't it be beneficial to both to make the agreement?

No, at no point were the USSR and Nazis allied. There were no trade agreements, no personnel support, and no treaty outside of the Pact. However, I think it is disingenuous to say that the USSR and Nazi Germany did not militarily benefit each other.