Correct Top Tube vs. Correct Frame Size

I need a bike with a top tube of about 50.5 cm. To get a top tube of
that length, I need to get a frame that is one or two sizes too small.
That is, I would have to get a 49 cm. frame, whereas my inseam would
indicate a 52 cm. frame. My LBS says that it doesn't matter that the
frame is so small, but this strikes me as being counter-intuitive. Is
the LBS right? Should I get the correct size frame and install a very
short stem?