Cheers, you've no idea how confused I've got about this. My LBS generally are absolutely excellent, but when I took my old P7 in there (99 model) for a service - they advised I needed a new chainset, as STX-RC was not compatible, something about the inner ring. I must admit, I didn't understand at the time, the point of changable rings, when they only fitted one crank, why my rings wouldn't be compatible. I don't think they were trying to "oversell" to me, genuinely, they've done quick jobs for free even when I was happy to charge (taking a spider of a bmx chainring).
The crank arms themselves are in good nick, and so is the sq taper BB, so it seemed a waste of metal to junk the whole lot.
All depends which version of STX-RC you have on your bike. You've mentioned that it the MC-40 version which was one of the first Shimano 4 arm chainsets with all three rings replaceable with the now common 104/64 BCD chainrings.
Some of the five arm versions did have an odd arrangement were the inner chainring was bolted to a special middle ring and not to the crank spider.
Your LBS is right to be a cautious, and it shows that they know about the peculiarities of STX and STX-RC.
I'll check on my MC-40 crankset later today but I'm pretty sure that they do have 104 BCD chainrings for the middle and outer and 64BCD for the inner.
Shimano did play around with BCD with some other cranksets, especially with XTR. They have used 102, 112 and 146mm for the outers and 68mm for the inners.