It's the first I've heard that learners can drive on motorways in the UK.
I think you and your missus had better read that new licence again and, if you're still confused, contact DVLA asap.
I think I know what the answer will be and in the meantime I'd advise her not to drive on the motorway with L plates or not until you find out for sure.
Please let us know the outcome. I for one would be very interested.
LGV and PCV learners can use a motorway, but that is because you now have to have a current full car licence to have provisional LGV or PCV. As said, car and motorbike learners can't use a motorway.