I opened an issue about it in the past at https://github.com/i3/i3/issues/2971 . Apparently it's not on the roadmap, but someone posted an xdotool script in the comments that you can chain with every focus switching command in your i3config thusly:

  bindsym $mod+h focus left; exec --no-startup-id center-mouse

I've been using that and it fixes the issue for me, even though it seems silly that it's not built-in given there's a mouse_warping config setting.

That said, I thought i3's default behaviour was that it would only focus a window when the mouse entered it, not when the mouse was moving around within a window, so I'm surprised you're having that issue. For me I just got sick of my mouse being "way over there" in the odd situation I need it.