Maybe the same lab shouldn't even be testing both samples. Just send the sample from the victim to lab #A and same from the accused to lab #B and compare the digital results.

The two samples shouldn't be sent in together, there is absolutely no benefit in that. Plus the lab shouldn't know what they're testing so there can be no accusations of bias/manipulation (e.g. "this person is definitely a child rapist, if you guys find this DNA matches this child rapist goes to jail, if it doesn't' (wink wink) then they go free").

The anonymous digital results can then be shipped to the defence so that they can double-check the degree of similarity with an expert of their own.