I'm sure that what the dealer really meant to tell you was:
"Resetting the adaptive values and relearning the values for the new
transmission, which would involve a brief test drive, is part of the
service procedure for replacing the transmission.  I'm sorry we didn't do
this when we had your vehicle in for service.  We can do it right now to
rectify the situation if you'd like.  It should take about 30 to 60
minutes."

Sorry for the sarcasm.  It really troubles me when someone does a crappy
job and then makes like it's not their responsibility to fix it.  Once
cleared, the values should reset after several 1-2-3-4 and 4-3-2-1 shifts
after the vehicle reaches operating temperature.  If they never cleared
the old values, it could take quite a while.  And yes, the shift flare is
slipping the clutches in the transmission and is wearing them.

It's likely that the real issue is that your transmission computer needs
to be reprogrammed.  There's a technical service bulletin specifically
referring to the condition you describe.  It's bulletin number 02-40-001.
If you don't have one, register for a free account at www.hmaservice.com
and print out the bulletin.  Take the bulletin to the dealer and ask them
why it is they don't know about it.  

And while you're at it, ask them why it seems to be your responsibility to
reset the adaptive values on the transmission when Hyundai reimburses them
for this as part of the labor operation to replace the transmission.  TSB
06-40-005 should convince them you're correct on this matter, too.  

The TCM is covered only for five years and 60,000 miles, so its
reprogramming is your responsibility.  But in light of the troubles you've
had with this dealer's BS, you may be able to convince a manager to do this
for you at no charge.