I ran into this a few days ago while booking LHR-IAD-SFO. LHR-IAD was R~4, while IAD-SFO was R=0. Even though the website reported R=0 for the entire LHR-IAD-SFO trip, I went ahead and booked. As expected, the SWU for LHR-IAD cleared immediately, while IAD-SFO was waitlisted.
Therefore, even though the website is making this all annoyingly difficult, your SWU will clear based on availability of the individual segments. Now, if only the CPU system made any sense...