I am using my own loot tables and from my testing they are not compatible with Quark (no runes and ancient tomes).
I've tested this with commandblocks with and without custom loot tables and with a bunch of naturally generated dungeons. Runes or Tomes every other chest without custom loot tables, but none with them.

edit: If this is intended, can I please have access to the loot pools for vanilla generated chests to copy them? Within the jar are only the new ones for pirate ships and wraiths.

Tested with MC 1.12, Quark r-1.2-101

Runes and tomes are added to the vanilla loot tables in runtime. If you want them in yours you have to make sure you include them there yourself.