In addition to proper bolt stretch, you also want to be torquing to the values the mains were aligned with, and use the proper lube.
If you are just swapping bolts on the mains, and didn't do an align hone, it likely won't be straight, not necessarily because of the bolts, but because old FEs generally have misaligned/tapered mains LOL
Additionally, I have been leaving the washers off the rear main for a long time, align honing it that way, and torquing to 105 with liberal lube. It leaves you room for the head of the bolts without cutting another .100 or so away from the cap (although nothing wrong with a clean dress on the cap either)