I went with JLCPCB to fabricate these boards and was very happy with the quality. I emailed them beforehand to ask about how they wanted me to notate NPTHs that went through copper pours (usually this signals a PTH). In the end I added a build note to my documentation gerber which called out the drill diagram and I exported two different excellon files, one for NPTH and another for PTH. I also noted this as a comment on the online order form.
They also honored my request to place order number codes on the back side of the board to keep the front pretty. Due to process limitations they weren't able to drill directly through the copper like I wanted but they added a very small pullback to the annular and drilled through the exposed FR-4 which didn't present any problem for assembly. In the future it would probably be easier to modify my library component to present this part as a standard NPTH surrounded (but not touched by) a ring of exposed copper to preclude the need for all these notes.