Hmm... In your photo the robot seems to be at around 0,-90,90,0,0,0 and your screenshot says something very different - are you sure that they belong together?
Aligning the mastering indicators (the white/black marks) won't lead to perfectly "round" values, though.
As far as I know, there is only one set of mastering information with no way to revert. You can however check the mastering and then decide whether you take the new values.
Regarding the EMT, unfortunately I haven't ever used an EMT with a KRC2, only the hacky way. The tool for KRC4 (EMD, they changed the name from German to English) looks different because it uses EtherCAT as the bus system. 2.5k seem a bit much to me, though. I think they cost around 3k EUR completely new.
Best,
Johannes