I'm going to say he was telling the truth. I'm in CO so they know what to look for. I'm sure they love the TX buyers though, they seem to not know that a mechanic can plug into their car to see if it is modded =). An ECU check is not hard to do and takes literally less than a minute. I'm trading my '09 for a '13 and when I did the "trade-in" inspection they knew I had a stage one tune (accessport was at home and I'm changing it to 100% stock before trade in). The dealer gave me 2 numbers and for me it was, "18K as is, 20K if back to stock so we can make it Subaru Certified". Leaving evidence of modding makes resale value go down, at least up here.
Also, I totally agree it was a jerk move to leave it untuned with DP, but it is why I won't buy a used WRX/STI in CO. I'm changing mine back the right way.