Hello Jon,
In my experience, the Hoboken 12-string truss rod covers may vary a little from guitar to guitar. Some are slightly rounded on the pointy end, next to the nut, so they'll clear the tuner ferrules. Some aren't.
The ones this eBay seller makes are all Westerly-era size.
So for my Hoboken 12-string F-212 I had him make one 1/8" larger all around, and I asked him NOT to drill the screw holes for it.
I had already replaced those miserable Guild six-on-a-plank tuners with Grovers. But the Grover ferrules are larger than what Guild put on them, and though the 1/8" bigger replacement covered the dual truss rod slots just fine, it butted up against the ferrules and thus wouldn't lie flat.
Rather than sanding the pointy end, as Guild sometimes did, I simply faced the truss rod cover the other way, with the pointy end toward the logo, away from the nut. Voila! Works just fine, no sanding necessary!
Once I'd positioned it properly, I measured and drilled my own screw holes to match those on the guitar.
This guy does really nice work, IMHO. When you write him, mention my name and the fact that you're getting one made like mine, 1/8" larger all around than his standard size. He'll remember the job I'm sure.
Good luck!
Glenn Jones
