well I don't know why SIW2 choose one bootmgr over another, you have to ask him about.
However both bootmgr files are identical in code and file version.
The only difference is in the code signing here. One seems to have a time stamp one not.
Properly 2 groups of MS developers:
1th - for the ISO image files
2nd - for the winpe (boot.wim)
Both sign the files they use. So small difference in file sizes occur.