As other comments suggest, setting the height at 100% solves the issue, but introduces many others. What I found out is that it is worse when the keyboard is opened and closed.

Other thing I noticed on the header of my application, which has position: fixed but is being scrolled out of the view, is that if I get the bounding client rect the Y value is negative, so I tried something like this:

const handleScroll = () => {
  const headerElement = document.getElementById("app-header");
  const {y} = headerElement.getBoundingClientRect();
  if (y !== 0) {
    headerElement.style.paddingTop = `${-y}px`;
  }
};
window.addEventListener("scroll", handleScroll);

The problem here is that after ~800px are scrolled down the Y value is 0 again but the element is still outside of the screen, so this fix becomes useless.

I see this issue affecting multiple pages, from their own apple website to this stack overflow page and basically every page with a fixed element on it, but I cannot find this issue being tracked by Apple. Is there any support page where this has been reported?