I think the Vaughn situation is tough. When did he come off the IL from the hamate fracture? I'm not sure he's actually been eligible for longer than Yelich, but your point about him getting fewer ABs stands.
The two things that mitigate this somewhat for me are:
1) Bauers has maybe been our best player this year, and he's going to get the more dominant side of the platoon. Obviously, you could let Vaughn DH and sit Yelich. He's been worth a full win more than Christian per bWAR. But I do wonder if part of Vaughn's success is that he's being used right. The Brewers are good at this, and I'm not sure him as full-time DH produces a one-to-one translation from his current numbers.
2) Vaughn's still played in 100 games (108 for Yeli). PAs are obviously a better measure, and Yeli is clocking like 150 more this year. I think I'm with you in that I'd like those numbers to be more even, but Vaughn also has a lot of value in PH situations, especially given the need for a power bat in those spots, and he often has been subbed out halfway through close games for defensive purposes.
All of which is to say, I think you're right. The Vaughn-Yeli splits are too lopsided toward Christian. For me, though, I also think we're not that far off from a much fairer balance (giving Vaughn 50 of Yeli's PAs makes it feel a lot better), especially when you consider that there's a legit argument for trying to get Yelich going and that Vaughn's limited PT hasn't hurt his overall production (you could argue it's helped it).
I'm trying to decide how much of wanting less Yelich PT is a hindsight thing (meaning Murphy's made defensible decisions) and how much is just stubbornly sticking with Yelich (which would mean Murphy bad).
I'm slightly more in the camp of the former.
EDIT: I say all this as a big Yelich fan, full disclosure. He's been basically a league-average hitter this season, which is far from his MVP peak (and way less than you want from a DH) but also from being the black hole some would like to claim.