Here on HED Ardennes Plus (20.3C):
What tire pressure do you run at what weight? I am 70kg and run f4.0/r4.5 bar with 25mm 4000S II on 21C rims (real width 28.5mm) - that feels a lot better on rough roads compared to 23mm tires on 17C rims. If the same low pressure is possible with a 23mm tire I would change, too.
Did you pick the Light Bicycle 21C rim? Meanwhile there are quite a few 21C/28mm wide options:
Light Bicycle RR36C02
I choose Light Bicycle 45mm for my front rim. Rear rim is still a 17mm inner width waiting for replacement later as it still serve me fine though.
That was on 85psi directly after mounting the rim (just to make sure the tire pop in securely at first). I only weight 68kg so i ride at 70psi on front wheel at the moment. I come from rim a lot narrower so 23c on this low pressure freak me out at first but it's clear that i can reduce it further so i'll slowly reduce pressure on every ride.
Are you sure your 25c Continental is only 28.5mm wide? That's only 1.2mm wider than my 23c. My Vittoria Corsa G+ 25c is 29.3mm wide but it interestingly has the less height than the 23c Conti. That maybe the only case i've seen Conti run narrower than Vittoria (but a lot taller i assume).
On my 17mm inner width rim. Conti 25c is both taller and wider than Vittoria 25c.
EDIT the typo number*
What was the weight of the rim? 460g as stated? Only 20g more than the 36mm rim, maybe a better choice.
My rims are NOX S36R with 20.5mm inner width and I only run 58psi up front.
Maybe that's why they are a little thinner.
Here it's 28.6mm on a 20.3C rim with 95psi:viewtopic.php?f=3&t=136995&start=30#p1270126
But why the difference isn't 2mm?
The main difference to 23mm tires on 17C rims is the heavily reduced road buzz on very rough tarmac (the one that even makes your car tires really loud). Bumps are softened a litte but not that much - for that "real" suspension is needed I guess (Speci Roubaix...).
I think I also have to try 23mm on my 20.5C - maybe they run very well with 60psi.
The rim would also be wider than the tire then and offer best aerodynamics.
Here you can see 23/25mm 4000S II on different rims: The height doesn't increase anymore from 17.8C to 20.7C.