I think the purpose of sending BoJack to prison was part of the argument about whether he deserves redemption, or what he has to do to be redeemed. The show's answer seems to be "Yes, he deserves redemption, but not on his own terms". Not sending BoJack to prison would raise all sorts of questions about the moral centre of the writers. Regardless of the moral crimes he committed like sleeping with Emily, or ruining Todd's chance at fame, or turning his back on Herb, he also committed a series of actual crimes. He supplied alcohol to minors and nearly caused death by negligence, he deliberately staged a car crash and almost caused death by dangerous driving, he assaulted a co-worker, he dealt drugs and caused Sarah Lynn's death, he then wasted police time and lied about the circumstances of Sarah Lynn's death, he broke into several peoples' houses, the incident with Penny was
dodgy at best etc. For him to commit all of those crimes and not be sent to prison could easily be seen as the show shirking from confronting itself, which it'd done such a good job of up to then. BoJack's asked why he's being sent to prison and his answer is simple and all-encompassing: "Well, a bit of everything really". I think, by doing this, the show has made the point that the likes of Kevin Spacey, Harvey Weinstein, Bill Cosby (or Hank Hippopopalous) etc. don't deserve death, but they should at least be properly, actually punished and made to realise the error of their ways, instead of being protected by their status and wealth. BoJack's hardly as bad as any of those guys, but he doesn't deserve to get away with his actions either.
What I will say, though, is that it seems to be coming clear in the aftermath of the season that these final 16 episodes were supposed to be 24, and that Netflix's decision to cancel the show changed things somewhere along the way. Apparently season 6 would have followed BoJack's time in rehab and his journey to self-healing, only for the reporters to start digging into Sarah Lynn's death and for Hollyhock to find out what happened with Penny. Then season 7 would have picked up where 6B did - BoJack an acting teacher, the reporters getting closer and closer to the truth he's tried to keep hidden. I think that's why, instead of writing their way through a year with BoJack in prison, the show just skipped ahead to him being given time out for PC and Judah's wedding. I wouldn't be surprised if we were supposed to see more of Mr. Peanutbutter's reaction to Pickles leaving him for Joey Pogo, or Penny & Charlotte's reaction to BoJack being put on trial, or Diane and Guy deciding to get together, or Todd moving in with his girlfriend, etc. Netflix's decision to cancel the show probably resulted in these storylines being shortened and stated rather than explored and analysed. Emotionally, though, and logically, everything still tracked. I think if I can come away from a TV show understanding what it was trying to say then it's done its job. I suppose I view it similarly to how I view the end of Game of Thrones: Did they take as much time as I wanted them to? No. But did I understand the point the creators were trying to make? Absolutely. It's the same with this.
I think there's a difference between an ambiguous ending and an open ending, and we got the latter. If people want to come up with stupid theories about whether he died in the penultimate episode then let them - it won't change anything about your personal reading of the show. Heck, I'm a big part of the Game of Thrones fanbase and you'd be surprised how many people think Daenerys is still alive, or who thought that one character was another character in a mask all along. Stupid theories are just part of watching TV.