While it is possible that a particular tariff may require that a flight be "on one flight number, no connections, etc...", if the agent is able to price it, it is permitted. In fact, doing it by segment you could come out with lower pricing (occasionally, not often), with the eg SFO/IAD/SFO pricing as one RT fare basis, and the IAD/AMS/IAD as another.

Again, if it is bookable and priceable and issuable (without building a manual pricing record), the odds are 99.995 that is doesn't violate any tariff rules.