My experience in short checking had to do with getting my bags to clear a Carnet (customs documents for expensive equipment).
Counter check-in was certain that it couldn't be done, but Redcoat came along and pushed it through....but I had a legitimate legal reason for the short check.
Agree with LoganFlyer about checking bags through on a 'partner' airline. Last year, into TPE through NRT, 3x bags got checked all the way through (D1 cabin) on CI (a tier 3 partner).
But on the return, flying KE out of TPE through ICN (connecting onto DL metal: D1, on fully booked DL ticket), they were not having any of the 3x bags and I got to pay the $200 - even tho they are a tier 1 partner.