It looks like the pipeline that was run for the gen2to3 repo was the one that does not apply external calibs. Following is a comparison of the configs.

DM-30864 (gen2):

$ head -30 /repo/main/HSC/runs/RC2/w_2021_26/DM-30864/20210827T213443Z/matchCatalogsTract_config/matchCatalogsTract_config_HSC_runs_RC2_w_2021_26_DM-30864_20210827T213443Z.py
import lsst.faro.preparation.MatchedPreparationTasks
assert type(config)==lsst.faro.preparation.MatchedPreparationTasks.TractMatchedPreparationConfig, 'config is of type %s.%s instead of lsst.faro.preparation.MatchedPreparationTasks.TractMatchedPreparationConfig' % (type(config)._module, type(config).name_)
import lsst.pipe.base.config

Flag to enable/disable metadata saving for a task, enabled by default.
config.saveMetadata=True

Match radius in arcseconds.
config.match_radius=1.0

Whether or not to use the external wcs.
config.doApplyExternalSkyWcs=False

Whether or not to use the global external wcs.
config.useGlobalExternalSkyWcs=False

Whether or not to use the external photoCalib.
config.doApplyExternalPhotoCalib=False

Whether or not to use the global external photoCalib.
config.useGlobalExternalPhotoCalib=False

DM-30867 (gen3):

$ head -30 /repo/main/HSC/runs/RC2/w_2021_26/DM-30867/20210702T225251Z/matchCatalogsTract_config/matchCatalogsTract_config_HSC_runs_RC2_w_2021_26_DM-30867_20210702T225251Z.py
import lsst.faro.preparation.MatchedPreparationTasks
assert type(config)==lsst.faro.preparation.MatchedPreparationTasks.TractMatchedPreparationTaskConfig, 'config is of type %s.%s instead of lsst.faro.preparation.MatchedPreparationTasks.TractMatchedPreparationTaskConfig' % (type(config)._module, type(config).name_)
import lsst.pipe.base.config

Flag to enable/disable metadata saving for a task, enabled by default.
config.saveMetadata=True

Match radius in arcseconds.
config.match_radius=1.0

Whether or not to use the external wcs.
config.doApplyExternalSkyWcs=True

Whether or not to use the global external wcs.
config.useGlobalExternalSkyWcs=False

Whether or not to use the external photoCalib.
config.doApplyExternalPhotoCalib=True

Whether or not to use the global external photoCalib.
config.useGlobalExternalPhotoCalib=True

Somebody should check which `faro` pipeline is being executed in the processing, and replace it with the correct one if it is not the one that includes jointcal+FGCM.

Ah this got lost in the review queue. This is investigation is done AND so is the step to have the right version of faro automatically run per camera configs, so I'm just going to mark this done for you too.