The pattern is only partially reversed in corresponding high schools:
San Marcos High: 848
Mt Carmel High: 839
San Pasqual High: 835
Mira Mesa High: 815
IOW, much of the differences between scores in the prestigious Poway School District and sub-par San Marcos/Escondido schools can be explained purely by the race factor.
P.S. it looks like the problem is with 4S North specifically. If you rank all schools using non-hispanic white scores, Stonebridge and 4S North are ranked below median in Poway district, #90 and #93 countywide respectively (out of 450 schools). But since they have large numbers of Asians, their overall API scores look good. Conversely, San Elijo Elementary is #50 by non-hispanic white scores, but it has much fewer Asians and more Hispanics, so it ends up ranked slightly lower overall.