I don't mind them having a server-side search function that actually searches the entire thread. I do mind having a heavily-used shortcut hijacked to behave in a non-standard way.
I don't see the problem with this tbh. When you create a JS app, you lose a lot of the native features of the browser and it becomes your own responsibility to reimplement them in a correct way. As long as the site pulls it off flawlessly, this is ok to me.
And from what I have seen, discourse does do this well.
This is done to remain performant specifically when the website thinks infinite scrolling is a good idea. In my experience it very rarely is, with the Ctrl+F thing being just one of the reasons why.