Here's the card texts:

Parallel Universe
[Neutral] The Thing From the Shore F98 / Illustrator: Régis Moulun
[support] - Environment. Attachment.
Cost : 1
Game Text: Action : Pay 1 to attach Parallel Universe from your hand to a story card. When resolving struggles at attached story, count the total skill of all participating characters instead of the icons to determine the winner of each struggle.

Beneath the Surface, Eureka!
[Neutral] The Horror Beneath the Surface F38 / Illustrator: Adam Bray
[Event] - Research.
Cost : 4
Game Text: Play during your story phase, before characters are committed. Action : Choose a story. Until the end of the phase, if you win an I struggle by at least 3 icons at that story, win that story immediately.

I've been wondering if it's still possible to use the latter to win a story where the investigation struggle has been replaced by something else, e.g. a comparison of skills. In this example, since the icons have been replaced with 'total skill' do I win the story if my skill was higher by three or more?

Or is 'Beneath the Surface effectively canceled since I icons were never actually compared?

Or something entirely else?

My gut reaction is that Parallel Universe would make Beneath The Surface meaningless, because, as you say, there are no icons involved - only total skill. But that's just by instinct.

That is correct. Because BTSE says specifically 3 or more icons it is incompatible with PU.