I had the same set up on an IRS Bug.
I made a collar to set the cap out a little. I think I needed about 1/4 in. so the overall lenth of the collar with inside/outside step was aprox. 3/8" long. (only the 1/4 in. shows) The collar has to have a step to accomodate the inside diameter of the cap bore on the wheel and other end of spacer has to fit outside diamater of fitting flange on the Cap.
I don't know how much you have to take off of the axles for clearance, but if you can do it that way, it'll look cleaner.
I have flat hub caps on my chromies on a Speedster. I had to cut the stubs off a little for clearance on those.
It was easier than I thought it would be. I used a die grinder (Zip Gun) with a 4" dia. cut off wheel. Cut right through it (rather than Grind the matl. off.)
The only thing you end up loosing is the centered countersink at the end of the stub axle. It's there from production. You'll never need it. Unless you want to check the stub for true between centers. But... If you suspect it's bent, IT'S BENT. Replace.
Greg