You mentioned that your PBH is 87.5, but not how tall you are. I dont mean to dismiss Vince's expertise and opinion, bt I think that's an important part of the equation if you're looking for an "ideal" fit.
My PBH is 87.0, and I'm 6'-2". So long torso, short legs, and difficult to fit. If you're shorter and more normally proportioned than me, I probably wouldn't hesitate on the 55. Conversely, if you're a similar height to me and have a 87.5 PBH, I also wouldn't worry about the 59 working.
I have a gen 1 Clem in 59, that's very close to the newest 59 Atlantis in terms of fit, and I would NEVER opt for a smaller size. Standover is tight, but comfort and ride quality trum everything. Even now, the top tube is quite a bit on the short side - which would push me away from the 55. FWIW, I use large 2.3 tires, which further reduce standover, too.
The Atlantis is funny. It was the bike that originally drew me to Rivendell, but I have ALWAYS been berween sizes so, as much as I've wanted one, it's never quite worked out. (Actually, there was a 56cm 650b briefly, which I almost bought, but decided it wasn't perfect.)
I've been thinking about this next batch of Atlanti too, but think the smart call for me is to wait until the next batch of 57 Appaloosa.