All of the surface-mount headers are on the same 0.1" grid. To be honest, I just spread some flux on, align them by eye, tack them in place, and solder them on. You have to be careful, but they don't need to be super-ultra-crazy precise since there's a little bit of tolerance with the holes. I've never not been able to get the boards to eventually mate with each other, though sometimes it requires a little extra force or going back and bending a few pins here and there.
One of the Teensy's internal 5-pin through-hole headers (for the USB host port on the 3.6 or A25/A26 on the 3.5) is not on the same 0.1" grid. I think that's what you were thinking of.
I may have worried too much about the surface mount headers. At work we use some 10 pin 0.050" pitch dual row that are a couple inches apart and getting them close enough can be a pain. I had no trouble with the breakout board.