Source a previous model year S40's fork or move to 650B, which is what I did to get reasonable space for tires and fenders on my Gen 1 S40. Running 650B there's gobs of vertical room for a fast 38mm Schwalbe G-One Speed tire + P.B. ALX fenders in 45mm-ish. The fork crown is too narrow to fit the fenders without modification, but that's easy to work around compared to getting more room under the fork crown. It's my understanding, based on posts here on the forum, that the Gen 2 S40 fork better accommodates fenders than my Gen 1, with more space and decent attachment points for fender stay mounting.
Reports of the Gen 3 S40 fork's limited clearance strike me as an odd move for a bike marketed as being for all roads and all missions (i.e. loaded touring capable on rough roads in all weather), especially given the market's rapid movement towards road bikes with significantly more tire volume --- and, incidentally, more comfort, more flat protection, more grip in all weather and often more speed and better handling. A 700x30c tire is hardly large these days for what the market used to call a sport-touring bike. Is that an "adventure bike" now? Or, "road+"? Or, "all road"?
-Jack