Yes and no, the top mounts have a 100% stock housing and use external piping to make the 90 turn to the inter-cooler. To replace that turbo would require you to modify any new turbo that you intended to try and make any turbo you had modified nearly impossible to sell to anyone else.
Yes, that is a good point on the replacement and resale value. Never been a fan of putting all that heat up there though, which is why I went with a bottom configuration.