As you've found - pcblist, schlist, and (what is it, schliblist/pcbliblist?) are my favorite features across all of Altium. Eagle is finally at least getting there, but I've done thousand-pin complex programmatic pin swapping using just schlist and Excel.
IntLib vs separate schlib/pcblib - I prefer to design every library item as a component, where a library component gets put down on schematic and board such that if I put the right symbol and wire it up in schematic, the thing that shows up in the BOM can be soldered to the board in that position and work. For most passives, this level of integration isn't terribly necessary, and I DO use generic components for that. But even then - you have to know before layout time that your "10uF 0805 unpolarized cap" actually exists in the world, and "before layout time" means schematic.