You are confusing an engine and an idea.

GoldSrc is a continuation of Q1 engine but it's development is of separate lineage even from Q2 and it was a fully licensed agreement. Setting and ideas are all original for HL.

TFC is a re-imaging of TF from Q1 but it's codebase is separate from Q1 TF.

TF2 is a sequel developed in-house.

HL2 is a series of sequels developed in-house.

EDIT: Portal has the same core developers and the same game mechanics, but both the setting and script are Valve original.

Sure, Steam pivoted their path of a game developer studio to a game publishing house but that's doesn't mean they never did anything themselves.