Offhand, I would try some sort of liquid sealant applied to both sides of the seams of the rainfly. Or try seam tape - what have you got to lose? Do we know that this REI employee does in fact know what he/she is talking about?
Storage conditions vary. Heat is especially hard on sealed seams.
One thought - how about using a sheet of seamless plastic sheeting as a rainfly? A lot would depend on the configuration of your tent. It would probably look odd, but might be quite effective.
I don't think that "non-REI" tents will be different with respect to water sheding....
one or more gifts or other benefits from the co-op.