So in a way, he is the defensive coordinator without the title. His responsibilities will be shared with Bill Belichick and other defensive coaches. It's pretty unconventional these days for a team not to have a defensive coordinator, but this is something Belichick has done before.
In 2009 after Dean Pees left, Belichick ran the defense for two years until Matt Patricia was ready to take over in 2012. Belichick gradually gave Patricia more responsibilities leading up to his promotion and that seems to be what he's going to do with Flores.
There is the fear that Flores could leave sooner than Patricia, though. Flores was courted by the Arizona Cardinals for their head coaching position before they eventually decided on Panthers defensive coordinator Steve Wilks.