I don't believe Naughty Dog is the type of developer that would let something like that effect a central design. Aside from having some of the most dedicated creatives heading the games with little resource constraint, the narrative driven approach to the central gameplay they've adopted and kept since the first Uncharted basically demands that designing around 'speedrunning' is only going to conflict with what they're trying to achieve. If anything, there's only a need to be worried about the opposite. Their games are some of my favorites of all time, but they have become more and more constrictive for player agency in terms of what is allowed at what time, what options you have during specific sequences which are essentially 'walking scenes', or close enough. I'd like TLOU2 to address more freedom in every possible scenario, so that we don't have to play hide and seek in a boss battle, or snipe to protect the exact same route of the people we're protecting each time we play, etc. Considering how varied the game could be on playthroughs and their original intentions regarding each battle being a real, dynamic test of tactics and skill, I have no doubt the sequel will do so much more in this regard. If it is even close to an evolution from UC1 to UC2 in terms of gameplay quality, it may be the best damn game of all time, story be damned.
Anyway, tangential rant over. You have nothing to worry about. A speed running trophy is just a fun thing to add in for people who have played the game and want to challenge themselves in a certain way.