This particular bug (from the OP) only affects games that use a lot of rapid mouse and keyboard inputs over the period of an hour or two.

And it only happens (weirdly) when you launch from steam, but have Steam Overlay turned off.

When launching from Steam, there is a layer that captures all keyboard and mouse inputs before they get to the game (for example, for capturing hotkeys to show the steam overlay). A separate layer called vulkan-steam-overlay (that is responsible for rendering the overlay over the game) periodically clears the input buffer so it doesn't get too big. If steam overlay is disabled in settings, the input-capture layer is still used, but the vulkan-steam-overlay layer is not used. So the input buffer captures all inputs and never gets cleared, it gets so big it needs to start paging to disk. That is what introduces the lag spikes after an hour or two.

Launching from Lutris doesn't use that input-capture layer, so that's why it's not affected.