The underground portion would be the same as the subway where you will enter through a fare gate. The surface stops will probably be like GO/VIVA where you will have to tap on.
I've done surface-to-surface-to-surface a bunch of times and it's always recorded as transfers. Pretty easy way to do a return trip on one fare if you have the right connections.
Peek inside Midland station while on a Line 3 shuttle bus today and it looks like the fare gates have been installed and turned on at the main entrance. Should be in service relatively soon.
All stations that have presto readers will get fare gates in 2017 after all the stations that don't have presto available yet gets them by the end of this year.
Dufferin actually is based out of Wilson. Mt.Dennis and Malvern are well into installation on their buses while Eglinton and Birchmount are the last division to receive readers.
I was riding the 505 earlier and a SUV just charged right through open door at Yonge and Dundas. Too bad for him there was a police cruiser right behind him and pulled him over right away :D