I had not read Matt's post on Rollison, and will give it a whirl. Thanks for sharing. I'd say with a middle reliever who has poor peripherals (even if they have a good explanation), it probably takes multiple successful seasons to feel good about notching him in the W column. Should he enter the W column, that would mean that the Cubs' pitching infrastructure turned a former first round draft pick into a useful middle reliever. Mazel Tov, I guess.
Correlation does not imply causation, of course, but this is notable for being the year in which Zombro was given a more significant role in MLB pitching operations. It's hard not to look at the garbage heap of broken MLB pitchers this year and not ask the question of whether Zombro (or as Matt points out, the philosohpical divergence between Zombro and Hottovy) is responsible. Taillon's season is a data point here for sure - I'll grant he's been a bit fringe since his TJ2, but he had been very serviceable for the preceding 2.5 seasons.
You're also right that the 2025 bullpen outcome is the best success story for pitching under Hoyer as POBO. Given the aggregate track record he has, and the complete failure to build on that success productively, I'm comfortable concluding it was a fluke rather than a stroke of genius. Boyd basically just got less hurt than he previously did. That's an example of them taking a good risk that clearly paid off.
With respect to the non-Zombro sources of blame you list:
1. I'm not sure the Cubs have spent less on free agent pitchers than other non-Dodgers organizations that have had success int his era, certainly not than Milwaukee. They've ignored pitching in the draft, but that's plausibly because the drafters (and Hoyer) are aware they have no pitching development to speak of.
2. Injuries definitely contributed to this year's outcome. However, they are sadly a major part of the game, especially the pitching side, and the organizations that are able to weather the storm have superior pitching development. Milwaukee, who you mention, has dealt with injuries to Woodruff and Burnes in recent years and ended up fine. Their bullpen (and pitching farm) is so deep that they plausibly would not suffer for losing Megill, Uribe, or both. Lastly, it's reasonable to ask the question of whether the Cubs' conditioning regimens or medical staff are behind the league.
3. No arguments here - they're definitely way behind the game on, at a minimum, everything to do with pitching. I think after 2026 we should be asking ourselves whether Zombro is a part of that.