OK, if the plan was to install new high compression pistons, I would expect a good mechanic to measure the cylinders (with torque plates, btw) and not just throw new pistons into used cylinders, no matter how many or few miles were on the engine. A lot of Harley shops just take the crap out of the box and slap it together, so at least you've got someone working on your's who seems to understand the right way to do it.
As for the entire cylinder taper issue, if you go back and read some of the information on this and other sites concerning the 110 jugs from 2007 and 2008 you will find that they were coming right out of the factory with huge amounts of taper, and I also remember a tech posting information that his dealership sent back 7 sets of cylinders they checked right out of the box that were out of tolerance. This was just one of the many quality screwups Harley inflicted on folks in those early years of the 110, along with the cylinder liner movement issue, crankshafts from hell issue, ACR issue, ad infinitum.
If you trust the guy working on it, let him get the jugs bored and honed to the next oversize and proceed with the work. If you don't trust him, you probably should have found someone else to work on it from the git-go. Just sayin'. IMHO, the folks who deserve to have the BS flag waving at them can be found in Milwaukee.
Jerry