If the Mouseflow Single Page App integration doesn't work for your website, then you can apply your own custom code alongside the Mouseflow script.
First, you need to ensure the window._mfq object is available:
window._mfq = window._mfq || ;
If window._mfq is available then you can simply push an update to Mouseflow whenever a new virtual page is loaded:
// When a new virtual page is rendered