Let's say I activate using a KMS server and then upgrade it with the Media Center key from Microsoft, will it completely overwrite the old activation to the point that Microsoft can't in the future detect that I previously used a KMS server to get activated prior to the Media Center activation? [Assuming that I use slmgr /ckms before using the media center key.]
No, the MCE key creates a whole new activation. There is no risk of your copy being invalidated in the future.