I don't know... They should know better at the store. But some AE folks are better than others.
What we ended up doing for me was checking brannock, which is a solid 8.5D and even on the slender side of D. But the 5 last smooshed my pinky toe and the outside of my foot. The AE rep instantly knew I had a high instep. We tried every combination of 5 last, a size larger, wider, etc. The larger is just too large, the E my heel swims around, in D and my instep pulls up the vamp enough that it squeezes at the toe. You'd THINK I would feel it on the top of my foot, but it's the outside that hurts because the instep pulls it out of shape.
My last is 201. It works like a charm. I mean, so close it was like it was made for my foot. The 333 last was also great for balmorals (bluchers are loose so I have to wear thick socks) but they don't make anything 333 anymore.
So, for you. St Johns are 1943. It's an AWFUL fitting last for me. Worse than 5 last. Literally I can't even get my foot into an 8.5D on that last. Also, since they are monks, they'll fit differently than everything else on the last, so it's a bad place to really judge other shoes. But, if you fit a 5 last you will usually fit a 1943, if one pinches the other will usually also pinch.
The Higgins Mill is a boot last. That's supposed to be wider in the forefoot, so I don't know why you'd be rubbing there like in the St Johns. But it is the "sleeker" boot last, so higher toe and theoretically a wide toe, but not necessarily higher instep. I honestly think you might have an instep issue if she actually measured you on the brannock as a D and THAT is pinching your toe.
I suggest you go back to the AE store and tell them your problems. Ask maybe to try on something with a 201 last (Jefferson, Bartlett, Stirling boot) and maybe ask if your instep is normal or high. If the brannock device says D, but you think E, something else with your foot shape must be causing it the issue.
I've really soured on AE, but I own a lot of their shoes. They F_ed up pretty much every new pair I ever ordered, but their customer service was always exemplary. Lots of apologizing, a couple of $100 gift cards, and very hard work to try and make things right. They SHOULD be working very hard to make you happy and fit well, unless that part of the company is also going downhill. I think your rep just didn't understand your specific problem and you need to guide them a little. They usually want to help.
All that said, with this problem I bet you will want to avoid the Hamiltons. But there's no way to know until you try them on.