I'd actually say that's extremely convenient--I'm not sure what the problem is? As it stands, the buses exit/enter the 407 at Keele, then go all the way down Keele to York Blvd where they unload, wait, load, and depart back on that route. Now they'll exit at Jane, travel a very short distance, service the subway station, and travel a short distance again to get back on the 407. This means:
1) For York students, at times of day with less traffic, this will come out to be just about even in terms of travel time; Keele is clogged between the 407 and York Blvd during most of the day, so having to take an escalator/elevator down, wait for a train, go 2 stops and head back up will be within 2 minutes of the bus trip time, I'll bet. Also, keep in mind that the current plan is for that subway ride to be a free transfer if you get off a GO bus and tap off the subway at York, or vice-versa, this is why TYSSE is getting tap-out faregates from day one.
2) At times of day with more traffic, this will save a significant amount of time on the trip. The bus can sit in bumper-to-bumper traffic barely moving all the way from 407 to Steeles, that stretch can easily take 10-15 minutes during rush hour when it gets especially bad.
3) For passengers not going to York, but connecting through to the other 407 GO Bus (West-East or East-West) this will save a HUGE amount of time! As it is they have to sit in traffic all the way down to york, wait for the other bus, sit in traffic all the way back up to the 407...or use keele/snidercroft to switch directions, where they have to cross a busy intersection twice and wait outdoors for a bus, plus not necessarily get a seat due to the buses being busy leaving york. Instead, they will hop off right at 407 station, which is barely a detour from the 407, walk to another bus platform, get on, and continue their journey with MUCH less time lost. This is an overlooked benefit to the change--through passengers along the 407 really see a big gain.