I cant help directly, but I have a similar issue. My LCD monitor is in 'normal' orientation however, with the mayflash wii bar mounted horizontally at the top. My crosshairs are constrained to the bottom left quandrant in mame-2003-plus at least. (pi 3B+, latest official retropie build).
so no help but fyi you are not alone! I just came onto the forum to search for the same issue
good luck finding a solution! Everyone here is amazing so hopefully there'll be an answer.