I know your pain!Burger Kin
It's kind of the caveat with all small bass drums. I actually gig with a 14" tom tom set into a cradle. I had to engineer it so that the bass pedal sits back a bit ****her than it would normally if it were to be clamped onto a regular bass drum wood hoop so that it doesn't hit the rim. I use a Tama Iron Cobra shaft and beater with a DW 5000 Turbo pedal with the footplate. The IC beater head has an adjustment that allows me to compensate for the increased angle of the shaft-to-drumhead relationship so that it makes full flat contact with the head.
It's always a "Rob Peter to pay Paul" kind of scenario. In other words, you switch one thing and it just transfers the problem to another area. I don't have the problem of the shaft knocking into the wood hoop as you have described, but I can see how it would happen. Honestly, you might consider getting some lower profile wood hoops made....or, possibly notching out a place in the hoop (which I would only recommend doing with a new 18" hoop because a vintage 18" hoop is too precious!)
My solution for 18" bass drums is to just accept the beater hitting higher on the head. The sound of an 18" bass drum just isn't going to provide the fuller-spectrum sound of a 20" or a 22" bass drum. The 18" is kind of a "special" animal.