Look at it from the other direction, and I think it will clear up rather quickly.
They did not have his DNA when they searched his car. (And maybe this is causing your confusion. You said: "They would know if it was EA's DNA." But no, they wouldn't, as they had not previously taken his DNA.) They found male DNA and want to determine whose it is. The reason they would call it "unknown" is that, until they have a sample of his DNA, it cannot be stated that it was his.
In the sw to get permission to take some of EA's DNA and see if it matches, they have to provide a justification for doing so. "We found unidentified male DNA in our search" would be that justification.
Also, my guess is that they have other DNA places, that they prefer not to mention, and for which they would like his DNA on file already. (I'm thinking of the trash pulls, for starters.) This mention then allows them to get that DNA, without mentioning what else they think they have.