In my boards I seat the socket pins lower - they have a stepped shape so there are two possible hole sizes you could use that would put them at different heights.
With my configuration, the nipple still goes through the whole.
Using something like the Harwin socket would be more expensive, but then these are IN-18 tubes. So for me the choice is between Harwins and a smaller neopixel, or those D-SUB connector style pins and an acrylic template to get them lined up properly.
Personally I would go with Harwins and a smaller neopixel.
I don't have a dog in this fight, but an option would be to have a separate tube holder board which connects to the main board.
That offers the advantage of creating different "holder" boards for different tubes without having to modify the main board. The "holder" boards could be as far from the main board as necessary to provide clearance (the interconnect could be as simple as just wires, no connectors), and the layout could allow LEDs to be mounted on either the main board or the "holder" board. For tubes without vacuum nipples on the bottom, the holder board could be installed flush, only increasing the tube height by the PCB thickness.