It's an artifact of SFO-SAN + SAN-ORD fare combinations often being cheaper than AS SFO-ORD through fare filings (but not always). This is likely due to AS fare matches of WN on SFO-SAN (fares start at $39) and SAN-CHI (fares start at $77). Since it's a fare combination, upfaring from Saver to Main means you will get hit with upfare pricing on each segment. In case below, $40 + $40 = $80. The fare difference between Saver and Main on SFO-ORD when booked on a single fare component is $40 (as demonstrated below). Some airlines have fare combination restrictions found in the fare rules of their cheaper fares that prevent/discourage such combinations (either allowing only A-B-A routing fare combinations, or requiring a stopover between segments which means +4 hour layovers).