I'm not sure if a tap-out would be needed at Highway 7, Highway 407, Pioneer Village or Downsview Park. Presto can be programmed to retroactively apply the co-fare - for example, if you take a YRT bus and then a Go Train, your YRT fare is reduced from $3.40 to 75 cents without having to tap off. At York University though, it would be needed if the free transfers are going to be applied, otherwise Presto has no way of knowing whether you got off there or at another TTC stop.
The notion of a tap-out being required is, as you say, not relevant if one is connecting to YRT, Viva, or GO, but rather for when one simply travels to 407 or VMC and doesn't connect to another agency...my understanding might be inaccurate, and this is probably still being finalized, but from what I know, since you're crossing steeles the $3.40 YRT fare would be added on for travel to 407 or VMC even just by subway, much as it is today when you travel north of steeles on a TTC bus. So, tap-out would be required for those trips where one doesn't connect to a bus.
And, as you mentioned, it would be required at Pioneer Village, York University, and Downsview Park for the sake of those 100%-free transfers to/from routes that used to serve York U...and at that point, they'll probably do it at Finch W too just to have the TYSSE be universal.
It should also be noted that this is all
somewhat a moot point--the TTC has stated many times that they intend to require tap-out across the entire subway network once Presto and the new faregates are fully deployed; partly to help combat fare evasion (one would have to jump the gates twice, not once), and to pave the way for fare by distance/zone. Similarly, these fare integration/co-fare/free transfer matters are temporary arrangements for the sole special case of the TYSSE...once Metrolinx's master plan for regional fare integration is out, and once they force all agencies to comply
or else, then there'll be a universal set of rules.