Is Passivhaus or PHIUS always the best way to build?

PHIUD is the Passivhaus standard for the US

A builder online had a question about the passive house certification. He was concerned about what the payback period would be for the added insulation vs better air-sealing. He is intending using an onsite applied foam in a flash and batt application between the studs and rafters. His thoughts are the air-sealing system is a more important factor in providing a better overall performing shell.

First of all, you are not required to build to PHI or PHIUS prescriptive standards. The vernacular architecture of historic homes is often a good starting point to find effective strategies. PHI started in Germany and PHIUS is an adaptation for the US. It lacks the good sense that local AEC professionals bring to the table. The new prescriptive values, see the link, is based on generalizations and assumption.

Taking into account your home's thermal mass, exposure, orientation, air-sealing, and micro-climate could yield a vastly different and better-performing home. Foam is a double-edged sword. It has good initial insulation and air-sealing qualities. As someone said earlier, if the dewpoint of your flash and batt wall or roof happens in the wall you may have condensation in the middle of your cavity with no place to go.

The foam also degrades rapidly losing the seal and insulation you are expecting. Spraying between the roof rafters is the area most likely to degrade. The chemistry and application of onsite foam application can have disastrous results. If sprayed too thick or the mix is off it may not cure properly. This results in noxious off-gassing and poor performance. I agree the economics may not pay off for the extra insulation. Maybe putting the savings into a heat exchanger, a better performing AC unit, or a different air-sealing system may be a better return on investment, ROI

PGH is a homegrown US sensible standard.  

The alternatives to a PHIUS home are of course the minimum state energy code home. They are much better than older homes and getting better and more expensive all the time. Another alternative is a Pretty Good Home, PGH. PGH is a middle-of-the-road approach. It is much tighter and more efficient than a code home. It also avoids the extra time and effort to certify a PHIUS home. With a Pretty Good Home, you could end up with a high-performing home with a much simpler design process. In the end, it is up to you to choose the path you want to take.