Does anyone have a good source for 2mm diameter LEDs in a through hole, round base, dome top format?
I don't think the flat-top (albeit low-cost) LEDs meet the OP's criteria for round-base and dome-top?
To be sure, it is possible to sand/smooth/polish flat-top LEDs into a dome-top but this can challenge one's patience!
That said, if you accept this level of detail modeling as part of the fun/hobby, another option is to use flexible acrylic fiber cable as the lens. You would still need to shape the cable end into a dome and additionally drop some colored transparent paint with the chosen lens color (unless you have white marker lights ). So called "end-glow" acrylic fiber comes in 1.0mm, 1.5mm, 2.0mm, etc. diameter and can be purchased by-the-foot. One "trick" is you can drive multiple fibers with a single LED which might apply to illuminating 2 marker lenses.
No doubt the ceramic stem LED is the closest-exit.