head to head
Neither is simply harder - they are hard in different places. Portal demands more execution; SpaceChem demands more optimization.

Optimization · Pure Optimization
The portal-gun puzzle game whose solutions are everything.

Optimization · Pure Optimization
A hardcore programming-in-disguise puzzle where you wire atomic assembly lines to synthesize compounds.
Portal leans Optimization (Pure Optimization); SpaceChem leans Optimization (Pure Optimization).
Portal leans clearly harder on execution.
Portal
Portal placement timing modest.
SpaceChem
Drawing waldo paths requires no physical precision
Same score on reads - which means the number cannot separate them. The difference is in what each one asks of you.
Portal
No adversary modeling player.
SpaceChem
No opponent; pure logic construction
Same score on variance - which means the number cannot separate them. The difference is in what each one asks of you.
Portal
Deterministic chambers; no randomness.
SpaceChem
All reactor inputs are deterministic and fixed
SpaceChem leans clearly harder on optimization.
Portal
Pure puzzle-solving optimization.
SpaceChem
Designing correct chemical pipelines that transform inputs to outputs exactly
A matching score does not mean a matching test. Two games can both sit at 10 on execution and demand completely different things of you - which is why the reasoning above matters more than the number beside it.