When I was a junior officer in the Regiment pen colours were reserved for certain appointments. I recall that only the CO could use a red pen and the Adjt would use green pen. It could vary, though, by regiment. There were only a handful of computers for word processing in the lines at this time and the primary users were junior officers who had used them at university. Corrections for letters, memos and orders etc would be done on the hard copy draft and passed up and down the chain. So having pen colours for each appointment made it clear who was saying what with each correction/question etc for the person making the corrections at the end of the line if they had questions.
Track comments does that now, of course, but this was a different time. Getting copies made was a big deal, so drafts could be passed along with comments/corrections for everyone in the chain and then sent back down. So there was a functionality to the pen colours at the time but that requirement has since disappeared, leaving the memory of a tradition in the collective memory fossil record of our traditions. So some in an army unit may still use a green pen as a the Adjt or CO but that is because they had heard about it and thinks its a thing. So it is a thing for them.
At least that is how I remember it.