The thing is, if you want to use full fenders, that aren’t split, and pass under the brake, unless you go with some unique long reach brake arm and a frame designed around those, it’s going to be tough to find a rim braked proper road bike that will do both 28mm tires and a fender at the same time, with “functional” clearance. And by functional I mean enough clearance so that the fender never rubs or ever touches the tire, regardless of how rough the road is and road debris isn’t constantly chattering and/or getting jammed up in the tight clearance between the fender and tire. Direct mount or standard mount doesn’t matter. Assuming Shimano just as an example, the clearance under their direct mount brakes vs their standard mount brakes is identical. And a significant advantage of standard mount brakes over direct mount for fenders is that there will be a sturdy support to pull the fender as high up into the fork crown, or rear brake bridge, as possible.
I was in a similar situation as you when I wanted a dedicated rain bike with proper road bike handling. Not cross, not endurance, but proper high performance road bike geometry. I surprisingly found that with, at the time (2014), the newly designed Emonda. It even had better clearance than the Domane back then, at least in the rear. So, with some mods to the full coverage fenders and a bit of tasteful MacGyvering it’s been the perfect rain bike for me, with 25mm Continental Competitions under full fenders with flaps that come within ~4mm of the road. Exactly what I wanted. 28’s however with full fenders/rim brakes would likely be a no go however.