He is way better off than struts, trust me..(except for holeshots)
As the bike get lower you want LESS and stiffer suspension.. you cant compres both ends 3 + inches like a stocker.. things are going to hit. Any suspension is better than none.. struts is a very rough ride.
Not everyone needs gobs of sensitive suspension.
And yes the tire will go up higher than the frame rail, if fender is mounted from above, rather than below, like stock.