"The builder says its fine,"

Yeah, and he's a nice guy, so it must be true, right? He's a BS artist. When are you going to wake up and see this?

The issue is the moisture that it's already absorbed. Painting it now is sealing it in, and it will want to escape when exposed to the drier conditions of a heated house. That means cracking paint.

So should we not paint it now? It's primed, but not painted. The transom and side lites have no primer or paint on them. Should we wait to do that until later? If so, when is the right time?

Yes, I'm aware things are going wrong. I'm not going to slander my builder, I'm just looking for advice on how to properly manage the doors with the situation we've been handed.

Would it help to take it off the frame, let it level out its humidity in a controlled environment for awhile, and then paint it?

Ha. I would say the door manufacturer is covering their butt by being extreme. But also may be trying to get out of further questions from you like "why is my door not closing" or "why is my door rubbing on the door frame". Wood exterior doors can move even after they have been painted and sealed. In 35 years in business we did countless wood doors and even after they were finished, 6 months later the door wouldn't open or it would be extremely tight in the opening. New homes have a ton of moisture in them. You can't stop that. He may just be trying to blame someone else for any problems you have with the door later on. Such as the painter. I have run into this before. As far as Doug fir, some framing material is made out of it. It is very resilient. If your door didn't get soaked by rain. You'll be ok. Wood absorbs moisture anywhere. Just think of that wood floor you posted a picture of on your other post. Think of the wood baseboard that was in that picture. It is absorbing moisture as well. Wood also dries back out. The moisture content isn't so high that it is going to want to come back out and push the paint off. If it is, you'll see moisture stains in the wood as it probably got wet. When we paint something with latex paint or primer, it is water based. It goes into the wood, the water evaporates and the solids are left to make the coating that you see. By the way, in many areas of the country (other than the southwest) you can't put an exterior wood door in and not be affected by humidity. Summer? (Hot and humid) Spring (rain?) Fall (rain/snow/moist ground) Winter? (Snow).

"Wood exterior doors can move even after they have been painted and sealed."

No finish STOPS the movement of moisture in and out of wood.

The finish can slow the movement, but NONE can STOP the movement.

The wood has 24 hours a day to come to equilibrium with the humidity it is exposed to, and for exterior doors only one side is even conditioned.