I have a M52 in 280AI that has a similar issue - I need to be about 40 thou off the lands to get 160NABs in the box. I am much farther away with 168 VLDs. This was slightly annoying to me at first - BUT - the rifle shoots really good with some jump. Really good. Every bit as good as a custom I have from a reputable builder (and LRH site sponsor). I'm willing to overlook the perceived loss of loading flexibility because I don't need it to make it shoot good...
I also have a M54 in 22-250 that is the exact opposite. It likes 50 gr pills, and I think I could seat them 10 thou into the NECK and still fit 'em in the mag. I shoot them 5 thou off the lands and that rifle shoots really well too - I sometimes wonder if it would shoot as good with more jump but have no reason to try.
I think Cooper uses the same bottom metal for each individual action (M54, M54, M56) and as such you are constrained in the longer offerings for each action. (Hope this reads clear - same bottom metal for cartridges in each action, not same for all 3 actions).
On a purely editorial note, with both of these rifles, I DEMANDED a mag fed rifle. Looking back I can literally only remember a few times where I jacked a second round in, and I think in those cases I didn't shoot again. All my range work is single shot. In reality, a single-shot model would probably work fine for me and would take away any mag box issues as well.... I just can't bring myself to it.