I'm just gonna mention here, but the items in the shop were correct for the previous version of Tethealla (that servers such as Ultima and Eden use), as far as I know. Percents, weapons and specials scaled correctly much like GC, but I don't think the shops have ever been close to accurate on Ephinea.
I had a look at the low level shops recently after I saw this and also got some 45% items as well. Didn't pay attention to the specials, but pretty sure you're not supposed to get tier 2 specials at this low level.
Yeah dynamically generated shop items is the best way to go about it. Unfortunately as with alot of the BB server side things we have to try to emulate how sega did things without actually seeing how they did it.