On the off-chance that any other noobs are having the same issue: The "Upload Plugin and Archive to Bethesda.net" XB1 function being greyed out when you try and make an Xbox mod I thought I'd make a note of the solution here.
I uninstalled the Creation Kit and Bethesda launcher and then reinstalled them - but rather than using the default suggested install location put them into my steamapps folder, In my case
C:\Program Files (x86)\Steam\steamapps\common\Fallout 4\
This not only allowed me to use the upload to XB1 function but it cleared up the hassle I was having with the creation kit not seeing the Fallout 4 .esm file so didn't have to dick around creating a shortcut to that.