My commuter has regular marathons 35mm, and ride very well. They are most likely lower than the 40s, but I’d look into trying to reduce the fenders by a few mm’s, can you modify the strut that bolts to the crown?
will be tricky for you to determine if x tires or x rim brings the tire lower, but maybe look into 35mm tires also, again might be hard to compare unlesss they are put on your rim.
could you show a photo that shows your tire/fender clearance? From angles that show it well.