Okay, gave a go at Doitsu's pagemap file, and, yup, it definitely works for me.
Even the roman numerals stuff works (which I'd never actually seen before, so, yay).
On most devices supporting KF8 (AFAICT, everything *except* the K3, though I haven't checked the K3 thing), the apnx file *HAS* to go in the sidecar (.sdr) folder though.
Since I'm doing this over SSH, I pushed the files in reverse to make sure the scanner didn't do something stupid (ie. pushed the sidecar folder, the apnx, and then the azw3).
And yes, the framework consumes the APNX file and builds the azw3f & azw3r couple.
(Yes, it's a Touch, but it's running on the 5.3 branch, results should be identical on a PW/PW2).
FWIW, I'm seeing Page 6 after a goto Chapter 3, too. Could it be because the id anchor (or however that thing works

) comes a tiny bit too late? No idea how the reader parses stuff, but there might be some tricky caching or stupid behavior involved.
I'm also not seeing a page number for the "Chapter 1" entry in the GoTo menu, I'm guessing for the same kind of reasons that the 'off-by-one' thing.
If I "GoTo" page 7, I don't see the chapter heading anymore, (ie. ==== PAGE 7 ==== is at the top), and I'm indeed on page 7. Haven't looked at the source, but that would seem to correlate with my hunch.