The HTML5 template is fine for testing, but not really good in production yet. Some browsers handle it well, but with others it can have weird results (e.g. on Linux with Firefox 64-bit and 4 GB of RAM I often have memory deadlocks...).
This should hopefully get better with Godot 3.0 or 3.1, there was some work done on it already. But I'd advise you for now to always label your HTML5 version as "experimental" if you want to avoid bad critics due to the performance.