I've also got 225/40/18's on the BBS RC's under my MkIV Wagon. No issues for me. I found a college kid unloading them so he could run some BBS 3 piece rims on his MkIV. Yes, there is wheel gap. There's wheel gap on all the SUV's I park between in the parking lot at work...
Are the 40 series harsh in comparison to the 65 series stock tires? Absolutely!
Should the alignment specs change if it is properly lowered? No.