Placing the SVG output directly inline with the page code I am able to simply modify fill colors with CSS like so:
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One way to do this is to serve your svg from some server side mechanism. Simply create a resource server side that outputs your svg according to GET parameters, and you serve it on a certain url.
Then you just use that url in your css.
Because as a background img, it isn't part of the DOM and you can't manipulate it. Another possibility would be to use it regularly, embed it in a page in a normal way, but position it absolutely, make it full width & height of a page and then use z-index css property to put it behind all the other DOM elements on a page.