Default [Q] Is a different file version used in PC companion than in the flash tool (Emma)?

Hi folks,

Sorry if I ask something that has been asked before, but I could not find the answer.

Is a different file version used in PC companion than in the flash tool (Emma)?
What I mean is, would using PC companion update with a country / region specific Xperia SP 4.3 file, and Emma with a general world wide version? Or would it be the same region specific file?

I had only problems with 12.1.A.0.266 FW after upgrading using PC companion (I tried twice), and have now downgraded to 4.1.2 and rooted it - after unlocking Bootloader.
I was thinking of trying 4.3 one more time, but using Emma Flash tool this time...