I’m in the ruins in Cozumel at the beginning of a New Game +. I’m in the first chamber out of the harrowing underwater passage, to the right of which is a braided rope door. When I try to open, it says I need to upgraded knife; which doesn’t make sense. I have all my other weapons, outfits, and skills from the first play-through, so why wouldn’t my upgraded knife carry over as well?

The knife upgrades do carry over. but you don't get it till you get the helicopter knife after crash.

Since in Conzumel, she still tech using her tutorial equipment

That makes sense. Thanks. On a related note, I’ve come to the conclusion that going after 100% completion is a waste of time. With both the Definitive Edition and ROTR, I was obsessed with collecting and doing every single thing in the game. The reward of which was nothing more than an acute , fleeting sense of accomplishment, followed by a feeling of wasted time. 

Seriously... What did all that running around, searching every nook and cranny, hour after hour, really get me? The exploration and hunting and tomb raiding and combat are superb in this game; none of which are actually benefited by finding every little journal entry or ancient necklace or child’s toy.

Starting now, no more of that for me.

I usually like doing it since for me at least, it makes the game longer and my diagnosed OCD won't allow any uncollected or un-visited map icons lol.

But when the 100% is currently glitched (much as it was the beginning of the previous two)  going 100% right now, achievement/trophy wise, is a 50/50 risk imo.