In My Games & Apps, I don't think even I have the Season Pass listed (I downloaded the Season Pass separately on release last year). I got the same as you, so I don't think it's that then.
For some reason, your FO4 is simply not updating, which may be due to the game (or MS) thinking you have the patch already. Do you use an external HDD? Were you ever prompted to download the 1.4 update after it's release (assuming you downloaded the previous patches, the first update notification you got after 1.4 released on consoles)? When did you last get an update prompt?
I'm going to assume that my Instant On, console off (background downloads) method should work. It isn't DRM or software licence related imo. For some reason, you had an interrupted update or you only half downloaded something, so it thinks you already have it when you actually don't.
Wiping your internal (or external) HDD may solve the issue, but that's pretty extreme too. This is probably why they asked you to uninstall Fallout 4 completely (I assume they did), not just the DLC. If you're using the internal HDD (and you have an external HDD lying around) you could try moving everything to an external HDD (or vice versa if you're currently using an external HDD).
It also may be a problem with your cloud synched data. It's a hidden mandatory function, so you'll have to go through some really painful conversations with MS support to get that sorted.
On Xbox 360, there was a way to access your download history (and consequently, your software licences). I'm not sure if the same feature exists on Xbox One (I had to go to accounts.microsoft.com to unsubscribe from ESO Plus), but there will probably be a way to check which software licences are tied to your Gamertag/Windows Live ID. Ask around, Google or tech support (last resort) and just double check to see if you have the licences (pretty sure you do if you can install Automatron normally).
Did you delete and redownload your profile (Gamertag) yet? That should get you the exact version of your profile that exists on their servers, so it all matches up. Again, that's a "if the Instant On method doesn't work" contingency.
So yeah, sorry to ramble a bit, but I'd say it's a synchronisation error of some kind. Nothing to do with DRM or licences.
Also, be sure to note your console ID and other specific information from the System(?) part of the Options. MS Support will probably need that if they're to seriously check your specific situation.
Edit : Oh, and obviously, when you had to redownload stuff, make sure you deleted Fallout 4, the season pass and Automatron (even your saves as they "should" be on the "cloud") then install FO4, redownload the season pass and then Automatron.
Chances are it'll be multiple patches, and for some reason, the Xbox One does not handle multiple patches well. It's a real PITA, but it's the only shot you've got.