I’ve always felt that if you’re going to cut the skipping, you have to also cut the references to it. It’s counterproductive to get rid of the sequence with the hypothetical “first-time viewer” in mind and then set up a situation where the first-time viewer now has to infer and recontextualize a reference to a now-deleted sequence that, to them, never existed in the first place. The edits are supposed to streamline and improve things. Leaving in stray references to stuff and then hoping they’ll do the heavy lifting FOR you is precisely the kind of storytelling decision most fan-edits set out to fix.
If you’re cutting Lightspeed skipping, just cut all the references to it. It’s the simplest, cleanest, and best possible way to go about it.