Not quite; all 3 engines share very similar folder structures. Even HL had a pak at one point, was removed when GCFs were still in use on Steam and no one bothered to restore it when GCFs were deprecated in 2013. In fact, Source (up until Left 4 Dead) lacked VPKs as it relied on the GCFs to extract the data. It didn't get its content put into VPKs til 2013. All of these folder structures actually still align quite heavily to Quake 1, as well.

Feb 11

Isn't Won HL1 was packed in .pak too ?