I'm in the process of laying ~500sq ft. of new red oak flooring, which is going to abut existing red oak flooring that has been down for 30+ years and finished with Waterlox tung oil. We're trying to go with a lower VOC option, and currently looking at the Bona Traffic HD, and tested their Amber sealer, but so far the color is much lighter than the Amber of the original floors.

We know we won't be able to match the color, and realize an oil poly would give us a closer match, but are wondering how we could use a lower VOC option and still get an Amber/finish similar to that of a oil poly, or Waterlox tung oil?

Applying an amber water-based coating will color the wood immediately. Coating
with solvent based poly-urethanes or oils will develop an amber color slowly.
You may be able to double coat the sealer to get a deeper color. The wood will also develop an amber color over time, so whatever coating you use the color will be affected by how much bright light it gets. The red/pink colors of the wood are fugitive so will bleach out.
Most finishes can be colored with trans-tint colors. Tinted finish requires more care upon application for a uniform finish.

From my tests so far, the amber sealer from bona is still quite a bit lighter after two coats then applying 1 coat of oil-based minwax poly. The color I'm looking for is a darker amber color so I'm not sure if if chasing the impossible with water based low voc options.

Finish with water in it does not give a rich color because as the finish dries the solvent based finish penetrates differently than the water that soaks into the fibers from water-base finish as it is applied.

Is there a way to get more color before applying the poly then?

Some mechanics use shellac as a sealer before the first coat of ambered finish.
There is a shellac called universal sealer that has no wax in it which may prevent another coat of finish from adhering.