I have Thunders and never stick with 53 OG Classics. I’d like to see it stick out more but it’s really not a massive issue.
I'm riding that exact set up now (with bones swiss and 1/8" risers) and am loving it. Tried a few different wheel shapes lately just to realize I should have never strayed from classics.
It's funny to me that based on this topic's posts the majority of people who have "That thunder baseplate problem" are people that ride Indy's. I already know what responses that comment will invoke from the cult of Indy but whatever, you know it's bs.
If you really want to ride thunder's but want more wheel clearance then grind down your bottom bushings or use 2 top bushings. It'll bring your wheelbase in a smidge and give you more clearance.