I have the same problem-- it's my first build, and I wasn't quite sure how wide my trailer would end up, and not wanting my axle too short, I bought it arguably a couple inches too long. My wheels stick out just about like yours with the fender mounted tightly against the side of the trailer.
I was thinking about floating the fenders out there away from the wall. I already have the fenders and wall drilled for mounting bolts, with T-nuts installed in the plywood outer wall. The ply sits half an inch outside the chassis, so I was already going to cut spacers from aluminum tubing to thread the bottom two mounting bolts through, below the plywood walls and into the chassis, just to cover the raw industrial exposed thread look. So I can use the same trick to cover the threads, set the spacing, and extend the fenders away from the wall, centering them over the wheels. I just worried that might not be sturdy enough.
Then I saw this pic, in LDK's Camp Critter build journal:
That mounting bracket can be fabricated as strong as necessary and will provide all the support needed while the aluminum tubing and mounting bolts will locate the fenders exactly where I want them. So that's what I'm thinking I'll try, but I haven't done it yet.
--Mike C.