Sword and Fist & Song and Silence are made by the same people as DR, with similar techniques and similar goals, so anything that is said for DR also works for S&F and for S&S.
As for PoF, the behaviour you described would seem to indicate a PoF bug, rather than a Refs incompatibility (since similar things would happen also without Refs). But then, I may just be paranoid against people that are unable to speak a decent English.
Did some testing with Sword and Fist. Was the last mod installed before worldmap and GUI (mainly to fill some kit slots and 2nd to test if it would work ok after refinements)
Monk: Gets all the new class abilities and all of your HLA's. I killed everybody in candlekeep and had a blast at level 42 lol
Hexblade: Gets its own HLA's and none of yours. A mix of custom HLAs with the standard fighter table is what it is based around and you get to pick some high level mage spells as HLA's. Interesting
Fist of Order: Gets your fighter HLAs
Duelist: Gets your fighter HLA's
Blackguard: Gets the standard fighter table plus the one custom HLA that the class is given which is summon fallen deva.
So on the face of it, it looks like your refinements and sword and fist fit well together, especially the monk changes and your HLAs.
As for SP collection I put it before refinements as you said and the ones I installed (blademaster, ninja, and deathknight) are all using your HLAs
Song and Silence, which I installed after like it says to in their readme are also all using your HLAs for every kit.
Since I did the workaround the Clerics and Druids are all using DR's HLA table and so thats working out well too. The bowslinger picked up your archer HLA table and not standard ranger which is nice and the justifier and ferelan picked up refinements standard ranger table. So
G3 has got their act together when it comes to kits for the most part
The pally that oversight installs holy liberator picks up your paladin HLA's as well. For now I'm staying far away from PoF kits, though I may add their druid kits since they were made to work with DR and with the workaround in effect....that might work.
so anyway thanks for a great mod!