In step 2, set your transformation origin to the baseline.
I have just noticed something strange. It leads me to believe that the mismatch has something to do with InDesign and/or the PDF rendering engine.
In InDesign the mis-match only appears when zooming in at 300% or above (for text size at 498pt!).
When exporting as a JPEG, the mismatch always appears.
When exporting as a PDF, the mismatch never appears.
Meanwhile, thank you mekkablue!
Edit: the “mismatch” is a not really a baseline shift, the stem sitting at the baseline is slightly thinner and another stem is not perfectly horizontal as it should be.
Edit 2: Maybe because the UPM value is so far off the “conventional” value of 1000, things tend to get messy?
Could you send me the .glyphs and the .otf file? Otherwise it is difficult to solve the problem.