Thanks for the idea but the order is determined by Inline::CPP when it creates the XS file in folder _Inline/build. Perl headers come first. However I did change the order of the includes manually (e.g. without re-perling, I went into said folder and edited the XS file). The first error (seed redefined) is gone (something tells me it will reappear if/when I make Perl call its seed) but the second error (e.g. namespace cv clashes with struct cv) persists (obviously).
My knowledge of XS is zero, but wouldn't using XS/XSpp require including those OpenCV headers? And still get the clash with Perl's headers?