That's pretty much what we have now, only with 3 settings. Since you'll be paying the energy upkeep, you'll want to have the shipyard fully populated, for full output.
Even in new colonies, the output will be static in steps, and all you'll need is 3 pop blocks (besides the food upkeep) to have the shipyard working at full steam. Especially at higher tech levels (which is the issue you guys are pointing out), where "spare" pop is higher (you practically have them on colonization), this doesn't seem to solve anything.

So, if I understand this correctly, the shipyard's output would be the industry output, but capped by values set in the XML?

The difference would be just in developing colonies?

well, it would be a ratio of the colony's industry, but yes with a cap. And yes, would affect mostly only starting colonies.
I still think we should go with manual pop assignment for shipyards, but in the mean time, it kind of achieves best of both worlds (in regards to static vs industry related).

Still keeping static output as default, right?

yes yes, it's an option that you need to add to the xml. So it won't change the default behavior