GoldSrc is based on Quake 1 code with valves own modifications and a little Quake 2 added in, if I remember correctly. I wouldn’t call that a “mod”, they bought a commercial license for the engine and made a game with it.
You’re trying to use this to say that valve are unoriginal? I really don’t think that’s a criticism you can lob at the half life series.
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.