is the audio in and the mic input the only way to get audio into maschine+ ?

Believe it or not I don't think so. I usually open the MP3 on my phone and run a line (1/8" headphone to dual 1/4" phono plugs) into the rear audio input on the M+. Set the sampler to record from the External source, pause the track at its start, set the trigger to a low threshold and press play on the phone.

I know it seems bizarre that's something so simple should not be built in but I bet the developers thought serious musicians wouldn't want to be importing lossy compressed audio like MP3s into their gear. That said, it certainly should have been added in one of the updates since then when so many users have requested it. Go figure...