Transliteration files and formats

[ReneZ]

If it's tied to coordinates, one would want a relative system so that if the resolutions of the Beinecke scans were ever changed, it could be applied to the new scans without a lot of reworking.

Not necessarily. The new coordinates would have to be re-computed in almost all cases, and this can always be done by a piece of software.
(For example: the grouping of pages in one image may change, the margins may change).

Furthermore, as long as the original images are preserved, they can even remain the reference.