It's CODIS, Combined DNA Index System.I do not know much about the various types of DNA but the expert I spoke to said if the MP and UP both have DNA in COTIS and they match it will show the match. She did not specify different types
I was unable to find a direct answer to whether autosomal DNA and mitochondrial DNA can be matched against each other (though I think they cannot). However, mitochondrial DNA can only be matched against female relatives. Thus if a UID woman has mtDNA in CODIS (or in this case more commonly, NAMUS), and her father provides a sample for comparison which is also entered, there will not be a match. So it's a great deal more complicated than if both people have DNA on file, there will be a match.
The below link gives a basic rundown on DNA types and matches.
AncestrySupport
support.ancestry.co.uk