So, I am somewhat confused now. I tested Godot 3's new HTML5 WebASM export today with a simple game, and the same system wide stutter (every 10 seconds, or so) occurs when I run it in Chrome and Opera.
When I run it in Firefox Developer Quantum, however, the stutter is... gone. Very strange.
When I export a Windows executable, the same stutter happens again every 10 seconds.
Whatever Firefox is doing, I'd like to know - butter smooth and no stutter for a minute of playing. How very odd.