Filed an extension and my spouse is late. can we still file jointly?

i filed for an extension before the dead line, and my wife and i were originally filing married separately. She missed the deadline and we want to file jointly. I am in the military and we have started filling out our information on my tax return to file jointly. Will she be considered late if she doesn't submit her tax return and we file jointly together instead? we also didn't know if it matters whose turbotax we use? I'd assume mine because its a military application. I want to make sure we aren't penalized for choosing to file on mine.