For some reason it apply some strange styles for half a second, that are not visible when option is disabled. So website design just for a moment on load looks strange.
So "in the end" the site looks OK? Did you exclude some CSS from being autoptimized? Or do you have CSS pulled in from another domain?
remove styles from parent theme that are in the child (parent theme styles minus child theme styles (styles in classes, but now whole classes completely).
that would require some advanced CSS-intelligence in AO, which I think would be to complex and frail to do.
Maybe the reason is that the order of styles and classes in optimized file doesn't match original order of files and css styles.
No, AO typically honors the original order actually.
My best guess; although AO aggregates & minifies the CSS, there is part of it which AO does not aggregate (reasons: excluded in settings, generated by PHP or external CSS), which is applied just before or just after the AO-CSS. The time between these different CSS-files being loaded causes the brief "Flash Of (partly) Unstyled Content".
hope this helps,
frank