I have this issue too, but I have the old boot loader, wont flashing official 4.4.4 give me knox?
Yes you will get Sammy 4.4.4 KNOX Bootloader. But IMO, it's not a problem if you don't mind not using HBOKERNEL.
I personnaly have 4.4.4 KNOX Bootloader and I don't have any problem using custom ROM based on Sammy Stock. I can use AGNi kernel or Stock Kernel without any problem.
If you use AOSP Roms, you have to check yourself if you can have issues with KNOX BL. For this point, I don't know.
Before flashing anything, please read a lot about bootloaders.