Well, you have a point here.
Anyway, a strange thing has happened during the last decade or so: silicon area has become cheap! Like really cheap, and really useful. They can do powerful "brute force" things practically for free, so it doesn't matter.
Yes, if you count number of total transistors used for a given solution, it's insane. But it's an irrelevant metric to begin with. Only the cost and capability matters.
A digital MCU-based SMPS controller is a straight solution from the first prototype to production for relatively complex, or otherwise special needs where there is no cheap and well known, working control IC available, or the analog control solution would be too large (from BOM viewpoint, cost, etc.).
Of course, there is no point in replacing an existing and good analog (most often IC) solution with a digital SMPS MCU when there is zero need to do that. Nobody is claiming that.
My latest thing had a kinda niche feature, utterly trivial to implement on paper, but not available in commercial ICs. The first iteration was analog (opamps, comparators, logic gates) with digitally-generated setpoints, the second iteration was digital SMPS MCU. Guess which one has a lot cheaper BOM, smaller board area, and a lot less issues with corner cases? Guess which one blew fewer fets during development? Guess which one needed only two bodge wires, instead of ten bodge wires, two SOT23 transistors and three 0603 resistors hanging in the air, taking hours to bodge in the 20 prototype units because of one trivial safety feature that was forgotten - don't turn the FETs on until supply voltage has stabilized?
Good thing in software is that you can add assertions, safety checks, corner case workarounds very easily and on the fly, and do a software update to all preproduction units. For me, the digital domain has been "safer" and in many senses, easier.
In my experience, I feel that I'm totally OK with every issue you have listed; really, the only thing I'm dissatisfied with is dealing with poorly written or broken MCU documentation, poor libraries and/or development software, and MCU errata / silicon bugs.