YES. You have a very valid point.
I think, one reason may be, the engine is already 1KR-FE, so need not write 1KR with it, but it does not seem like a very valid and strong point.
I cannot recall exactly what I wrote in the application form documents? Just plain engine No., or engine No. with 1KR?
I just checked details against my Vitz from online record available with Excise Islamabad website, and engine No. was not written starting with 1KR.