At some point it would have to. But personally, I recommend doing this on the Export side to avoid unwanted results.
There's a "Better Collada Exporter" for Blender (by Godot). In that, there's an option to triangulate your Blender models on Export. Also, there's an option to auto-apply Modifiers (if you i.e. use triangulation or other modifiers (like Mirror/Array) on your Blender models.
There's also a newer godot export filter currently in development. But I didn't try that out yet.
#2 10k faces for the main character may well be possible. The number of faces is only one of many variables which could pull down the frame rate.
- IMHO, GLES2 will be the choice for low end hardware. (Many low end cards support GLES3 but are very slow at it.)
- Fragment shaders, especially at higher display resolutions may have impact on the game. (Low end hardware has a very limited amount of shaders.)
- Lighting and shadows can have a big impact on performance.
- LOD: At the moment there's no LOD support in the 3.x Godot main branch. This is (hopefully) to be expected in 3.2. So you either implement it yourself or you have to wait for it.
#3 I am absolutely unsure. But it is possible that it appears one time together with Bullet as a selectable physics engine. Anyway as shown by Andrea it is always possible to do your own build. But I know only very little about this topic. You could propose it as a feature on godotengine github.
(Here's one of Andreas videos about nvidia flex in Godot:)