Just have the "debugging enabled" tickbox unchecked in the export dialogue, this will be the "release" mode and should run more smoothly. Don't worry about the "custom binary" file options in the exporter. This is only if you want to override the standard export modules with your own.
If you are creating a 2d game, there have been many reports of general choppiness in playback, and it really depends on many factors...OS, GPU drivers, etc. There is also no builtin v-sync in Godot, so you could try fiddling with your GPU v-sync options. Of course there is no control over what sort of problems the end gamer/customer will have with your game, but this is one of the joys of gamedev :)
In general, openGL drivers can be very inconsistent. I have given up on my laptops with Godot, as they were too inconsistent, but am finding I get excellent results on my old desktop with Win10/gtx560ti. I get a perfect solid 60fps, but on the same machine dual booted to Linux Mint, it has terrible performance with a choppy 20fps or so. Same machine, but different OS/Drivers! Welcome to openGL driver hell. Hopefully at the end of the year we get OpenGLES3 and more solid performance...