I haven't looked deeply into this, but in general when Waze picks a route this far out of the way, it is because there is a bad segment or junction along the faster/shorter route which makes the routing server believe a path does not exist. I haven't found this segment yet, but based on what I see in views like this one
, where there are many junctions which need to be deleted, that there is likely a segment which is set to one-way.
The one-way segment is supported by the fact that the reverse trip does
route you along Hwy 92/San Mateo Rd correctly.
I would go end-to-end along San Mateo Rd removing nodes which don't belong (have no street connected except San Mateo Rd), and make sure all segments are set to 2-way.