With a decent level of Wordpress and relevant plugins i've come unstuck with FPD. It's a great tool for custom designing artwork from the user perspective but it appears to work off pixel sizes. 

I have a pop up banner I want the customer to design. The design specifications are 1200mm x 2100mm. When it's exported the graphic is either too small and needs to be scaled up - which makes the image look terrible. Alternatively, if I make the canvas size and image much larger it's too large in illustrator.

Is there anyway to set the design so that when it's exported it fits to mm's in illustrator? 

This is the usual way of getting high resolution exports: http://support.fancyproductdesigner.com/solution/articles/5000593264-exporting-high-resolution-images. The technical difficulty here is, that html5 canvas and fabrics.js only support a DPI of 72. For products as large as yours I'd recommend using .svg vector graphics, as these can be scaled up without loss of quality, so the stage can be smaller then it would need to be with .png/.jpg.