You do not have to use r.js to optimize your AMD modules. Any tool that knows how to read AMD modules and how to produce a bundle from them could be used instead of r.js. I don't know if such a tool exists that is implemented in PHP.
If you are going to use r.js then you must have a JavaScript virtual machine that will run its code. r.js only supports Node, Rhino, Nashorn, or the browser. This is a limited list because r.js needs to be able to read files, and how to do this varies from platform to platform. (This also explains why browser usage is not generally recommended: the limitations in the browser are such that it can only be viable for restricted cases and not for general optimization.)
I'm not seeing the need for Node as being particularly onerous. The first projects I used RequireJS with were for applications backed by Django, which is a Python-based web framework. That's similar to your own situation.