I've got a Librands rack with sidescreen storage on the Plus Four. The centre screw rod is VERY slightly out of line with the theaded mount . I have run a tap to clean up the thread and I push the rack centre mount up with enough pressure ( not a lot) to get good alignment. Luckily it's a rare event so no big deal. A better fix would raise the rack into alignment so that's a job to do. It's only a VERY small change so not a big deal. The fiddliest bit is the spare wheel sliding down under gravity when fitting the centre bolt and spacer. I'll look at a way to prevent this. Something like an insert to hold the spare in place during rack fitting.
I just stuff a rolled up towel over the lower lip of the opening when refitting the spare and lining up the rack, added bonus is it protects the paintwork