Absolutely, you own the font that you have created with Prototypo and you can do whatever you want with it.
You can export as many fonts as you want with the full version. You can also do with the free version but you'll have the ability to modify your characters with 5 parameters instead of 30 with the full version.
Actually, it's not that way Prototypo works. We create letter templates with all parameters behaviours. But we want to give you an easy way to code your own templates and increase the possibilities to make custom fonts.
We have some issues with Safari for the moment. There is an issue opened about this, check it out on github.
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You can ask our team whenever you want, whether you subscribe to the full or the free version.