I'm here to verify. I think the actual question is "can you download a setup code of 1000 or greater into a remote that uses 3 digit setup codes?" The answer is yes, but only if you program the remote using JP1. The 3-digit limitation is just in the programming instructions (ie, the remote only lets you enter 3 digits when you program a code to a device button). The 3-digit remotes store the data in exactly the same format as 4-digit remotes. In other words, they both use 2 bytes of EEPROM memory to store the codes.

Of course, if the goal is simply to load an upgrade for which the official UEI setup code is 1000+, you could always use JP1 to create a WAV file where the setup code is a number below 1000. Then you could program it to a device button using the normal remote procedures.