My colored and probably controversial opinion (which turned into a bit of a rant, but I guess this topic's been on my mind lately, so, this isn't aimed at you specifically, /u/RiffyDivine2):
No one but me has control over how I spend my time, or if I charge for the use of my time and personal experience / expertise / general know-how. "No one" in this case also includes Bethesda.
You can say, "Hey, Chesko, come over to my house and fix my sink", and I say, "OK, that'll be $50 please, which is X dollars per hour of my time". I go over to your house, fix your sink, and you pay me.
You can say, "Hey, Chesko, write me a book." And I say, "OK, that'll be $5000 please, because it will take me X hours to write the book, and I charge Y dollars per hour." I write the book, you pay me.
You can say, "Hey, Chesko, write me a program in C# that does X", and I say, "OK, that'll be $5000 please", and we draw up a contract stating that you're paying me X dollars for Y hours of my time.
You can say the exact same things about a Papyrus script. You can say the same about a texture file, if I were an artist and painted you a picture that you could turn around and put in your mod. You could say the same about a model file that you could import into your mod, if I were a modeller.
Bethesda owns their intellectual property and prohibits commercial sale of files generated by their proprietary toolchain. That means I cannot go out and productize a mod I created and sell them on my website to anyone who wants to buy it.
But no one (Bethesda, my mom, Chick-fil-A, Piggly Wiggly, no one) can tell me, "You can't charge for your time and experience because we don't like it." That's just not how the world works, and it never has.
Bethesda can say, "We don't support commissions." Setting aside their own personal legal reasons for having to say something like that, there is a large chasm between saying (essentially) "We don't like that" and "you're infringing on some right we've reserved and we're going to come after you now based on a sound argument in our favor, like copyright infringement." They can "not like" and "not support" anything they want, and that doesn't affect you. This is why unauthorized Apple product repair stores exist. Apple can wag their finger all day and say "We don't support that, and your warranty will be void!", but there is nothing Apple can do if that repair store is simply providing a service based on time and experience and not infringing on any other trademark or copyright. Apple cannot do anything to me, personally, if I take time out of my day to repair my friend's iPod for $5. I rendered a service.
Regardless of how some will try to emotionalize the issue, or how they might personally feel about it and how it might "impact the community" or something equally intangible, this means that one-to-one commission-based work is completely legal, provided that it's clear that what you're paying for is work per unit hour, and not a product.
My time, and your time, is yours to both spend and to charge money for however you see fit.
Bethesda does not own anyone, and to hear some people talk, they make it almost sound as if they do.
Am I saying we should encourage this, or this should be an allowed topic of this subreddit, or that it would be good for the community, or anything else? No. All I am saying is that no one has any ground to come to you and say "You can't charge money for your time in this specific way."
Whether or not people will like you for doing it, or whether or not you are allowed to advertise these kinds of services in a particular space, or whether or not anyone will actually pay you, are completely separate issues.
Your time is your time. Charge money for it if you want, doing whatever you want, as long as it's not a crime. Whether or not anyone wants to pay for it is something for the market itself to decide. In my opinion, there is nothing grey about this at all, from a legal and ethical standpoint. It is only grey in that it is currently considered socially taboo in this particular community.
(Disclaimer: I have never created a mod based on commission.)