A scientist that I respect a lot who now has a title that sounds like it is probably a lot of work contacted me to provide more up-to-date documents, as the copies I posted expired several years ago.
The vendor is much more compatible with developers and even has a Github up that helps you walk through everything you need to alter the operation of your factory Orbitrap hardware. You can find this here. The things I highlighted appear to be totally absent in the new agreements, but it's a lot of words and I don't have time for all of them right now.
Please disregard this post as well! I'll make further corrections as I have time.