As the others mentioned you aren’t dealing a lot of holy damage for it to be amplified. A big problem too is the lack of multiplicative scaling due to working with low numbers due to level/gear so it’s harder to notice, too.
I’m fairly certain seal of martyr changed from holy damage back to physical, too. I was testing out JOTC & seal of martyr & seal of command damage, SoM seemed unaffected, however, back in phase 1 SoM was affected by JOTC despite not saying ‘holy dmg’ in tooltip.
The big holy damage ability you are using in that rotation of yours is crusader strike which is holy damage, but it’s 75% of weapon damage not 100%+.
SoR has some strange scaling and it tends to better a lot more from faster weapon speeds with spell damage instead of slower weapon speed, because while you do get more damage for a slower weapon speed, the gains are minimal. Similarly, because we’re dealing with a low hit of damage usually, you will not see particularly high gains from multiplicative +%holy dmg from it. However, I think you should still be seeing gains, in phase 1 I think JOTC added about +2 dmg per hit with SoM.
I should test out if aura mastery properly works with sanctity aura but the testing for a good sample size does take some time