Thicken stew/sauce twice with flour
A reaction that prevents starch from the same plant thickening if you add it later instead of all at the same time seems very unlikely. And anyway, a roux could be made with non-wheat flour even though it's not traditional - what do they think would happen then? Or if you make a roux on another pan and add that. I can confirm that works. 

There is a good reason not to add a slurry late in cooking - the raw flour flavour it imparts. That's why I'd use cornflour (corn starch) for late thickening.