Bypassing Version Check
The Vita will always write the current system version to the SVR field in the file. This means if you have two Vitas on different FW versions, and you put the memory card from the newer FW Vita into the older FW Vita, it will prompt you to update. To bypass this, you can make the id.dat file read only.
SceIoStat stat; stat.st_mode = 0x00002004; sceIoChstat("ux0:id.dat", &stat, 1);
This will make any attempt to write to id.dat fail including attempts to update the SVR field.
As a side effect though, every time you boot the Vita, it will rebuild the database. So be aware of that if you have any mods there.