I think what he's saying is that a set of caps that are not original to the block will not line up correctly with the existing crank bore line. This is true. Any replacement cap is 99% likely to need to be line bored and then honed in place. This is done by removing a few thousandths off the flat face of the cap (enough to accommodate the mismatch), mounting them in place, rough line boring the crank journals, then finish honing the journals. Process is much like that used to resize the big end on a connecting rod, just bigger scale and all done in one operation. Another thing that can throw a wrench in the works is that the tenon on the replacement cap properly fits the female tenon in the block. If it is too big, that's good because it can be thinned down. If it is too narrow and the cap can move side to side, it is a more difficult fix to use that cap. The fit needs to be tight, line on line or slight press fit so the crank can't walk side to side under load.
Not every shop is setup to line bore, while most seem to have a line hone bar. I had a heck of a time finding a shop that was capable and willing to fit replacement caps to my extra 340 block. There is additional risk in doing this in that the center to center distance of the crank to cam can be affected if done poorly. If they aren't enthusiastic about doing the work, find another shop.