Have both a tailgate and twin rear Toyota,
Tailgate, roof rack fitted and ladders work perfectly well, providing they are not left over hanging, handy when it's raining the tail lift to a standard height, twist the dampener and it raises more, not really an issue for window cleaning.
Twin, great for hanging thing's on the back doors, other than that, no difference.
Not sure about resale values being different, but I only ever buy Toyota, so never search.