When I import the 29891-RNC.drl file, the Fab3000 software correctly imports the .pho files, but incorrectly imports the drill file with an incorrect scaling factor.

Thanks for submitting a support ticket. Please remember Drill files are just XY coordinates without any formatting.  Here's what your sample drill file looks like,

Note: There's nothing in the drill file header which states the drill format (i.e where the decimal place should occur, nor what units to use either: inch or millimeter, or even the tool sizes).  These are things that FAB 3000 (and every other CAM tool must guess - unless that information is included in the drill header).  Here's a few links about drill from the support forum which should help, https://support.numericalinnovations.com/support/discussions/topics/14000003485

The drill file coordinates do not align with the Gerber.  Many PCB CAD tools output their drill files with different coordinates that the Gerber, so you need to perform align layers.

Here's a tutorial movie showing me correctly import your sample drill files and then have to perform Align Layers to move the drill up to the Gerbers,  https://numericalsoftware-update.s3.amazonaws.com/tutorials/2022-08-13_19-33-14_drillin.mp4

Note:  If you generated those Gerber and Drill files, I would recommend going to your PCB CAD tool and see if there are different options used during Gerber or Drill Export - to ensure both coordinates are the same - to prevent any additional steps (as above).

Thanks again.