Perhaps it might be worth clarifying what sort of "pt" does LilyPond use. Or did I just overlook this information?
For instance, run \version "2.25.12" \pointAndClickOff \header { tagline = "" } \paper { text-font-size = 12 } \markup { LOL } and either use -dbackend=cairo --eps, or produce standard PDF and decompress it (e.g. with qpdf). Look for the BT command in the resulting file. You'll find that the font size is actually ca. 11.9531, not 12. This would suggest that the unit used is rather the TeX pt (1/72.27 in) instead of the PostScript pt (1/72 in). The difference 12 * 72 / 72.27 - 11.9531 is quite close to 2/1024, again, although not convincingly close. AS