Just to clarify, skiplagged does do things a little differently.
For example: they saved me $300 flying from Japan to SFO because they booked me an additional leg from SFO to SEA. If you searched for the first leg on any aggregator (or the airline’s site), it was available but cost $300 more than booking the 2-flight itinerary to SEA (which would never show up if you searched for flights to SFO).
For what it’s worth, I agree that this form of pricing is absurd and should be illegal. The fact that skiplagged even exists indicates something has gone wrong.