This is part of what we call "MultiSkin". This means every plane in the air can look different, for example having different ID letters. This means the ID letter can not be naked into the main texture, else you would have hundreds of different 2kx2k skins in VRAM, which does not fit. So, there is a 2k x2k "main skin" and each letter is one say 128x256 texture. Speaking of ID letters only and one plane type only and no propellors etcs

you would then have 27 textures in VRAM, namely main texture plus 26 letters and could have hundreds of different planes in the air.
So, the BoB.exe has to place the letters at runtime and of course needs to know where/how large. The skinner painting the emblem must have done the historic research or had the research sent to him, so he is the right man to determine the position and size.
I hope that explains it, if not ask again and maybe add how you would expect it to work.
I played around with GIMP a bit and found out:
Opening the two files (main texture plus emblem) into two windows, "copy" one and "paste into selection" into the other works nicely

. BTW, it seems on all my computers I have the German GIMP version, so menu names are translated :-/.
A right click and then going onto the menu "Layers" I see two interesting items, one of which is the Shift T one BTW. One is called "size" and one "scale". One scales (good) and one lets you crop the new layer (which is NOT what I want). One allows a preview, actually you can move the corners and see the numbers in the dialog change (nice!) one does not. One only shows the scale factor (say 0.12 for 12%) and one also shows "Versatz" (movement/translation) which is what I need. Unfortunately none of the two combines everything I need

.
BTW, can GIMP record macros? If so, one might be able to "visually do it" and extract the numbers from the macro.