As Others have said, they look at flash count and if it doesn't add up to what they have on file back on the servers in Germany it can be TD1 flagged. They are not reading what is currently on the ECU, and flash count is something you can look up with VagCom or ODB11 currently. The ability to check flash count may have not been present on previous gen VWs, but the MK7 ECU is pretty high tech.
If you still want the ability to flash at home. IE and Unitronic I believe are the only two that offer at home flashes for the 1.8T. If TD1 is a concern, a piggy back tune is about the best you can hope for with Neuspeed or JB4.
Edit: IE Doesn't offer IS38 tunes on the 1.8T yet. So Uni may be your only option if you want at home flash. You can run bigger turbo with a JB4 though, it just takes time to setup the maps and may not give you as much power as a true flash tune.