i wasn't referring to any specific shop, since i have no idea where you live. sore arms and traps during the extended ride sounded like a fit issue, not so much the bike material and frame design, though i could be wrong; perhaps your form not relaxed enough. sore butt could be a matter of not having built up enough tolerance from time in the saddle. though it could be just that the saddle is not right for you, and the most comfortable and absorbant bike out there won't make your arse feel any better if that is the case.

that said, i'd make sure you're satisfied that the shop is giving you a good reason not to go with the beam bike, such as it won't fit you well or some other clear cut reason.

EDIT - rereading your initial post, IMO i don't think the first reason is a good enough reason not to go with a softride. if the bike ends up fitting you perfectly, i think it outweighs the inconvenience, as well as the supposed flex in the beam throwing off you pedal stroke (unless you judge for yourself that it is that bad).