The episode made it clear that Bojack had sex with Emily because things were going well with Todd, and so he acted out and did something specifically so that he could damage his relationship with Todd, so that when his relationship eventually falls apart (because Bojack feels that every relationship he is in falls apart) he can look back to the bad thing he did to Todd and blame that for why Todd left him, not because Bojack is inherently poison that drives people away.

It was less the fact that they banged and more that both of them had sex with eachother because they thought it would hurt Todd.

I feel like it could make sense as a way of saying like
you’re the one who has to hold yourself accountable, which is hard but it does get easier if you stick with it,
but yeah, a strange pairing