I will share a link in discord, thanks.
It certainly is possible to scale up using built in haxeflixel functionality but unfortunately there are some compromises to that approach. I added a couple of bits to the scale modes demo from flixel-demos to test things out. It's published here - https://jobf.github.io/haxeflixel-html5-pixel-perfect/
Using pixel perfect position or pixel perfect render (or both) it is possible to get close to the desired effect such that sub pixels are avoided when moving sprites on the horizontal and vertical axis. Notice the jagged movement of the sprite moving diagonally when either of those options are set.
However when rotating a scaled sprite there is still some extra interpolation going on. It is possible to have the scaling work the way I would like which does work perfectly when targetting windows desktop and probably other desktop targets too though I've not tested. The set up is shown here - https://github.com/AustinEast/haxeflixel-pixel-perfect - unfortunately this 'hack' does not behave the same on HTML5.
Also, apparently the pixel perfect settings are not always perfect. There's an example here - http://forum.haxeflixel.com/topic/953/pixelperfectrender-is-not-perfect-at-all/
So I was hoping webgl would be the way forwards. Except something funny is going on, either in the calculations I've used or somewhere in the base shader code.