Widening an existing road to add a lane for transit (bus or rail) is a Schedule C activity under the Municipal Class EA (i.e. the same as for a new transitway).
However, "localised operational improvements at specific locations", including "stopping lanes, access lanes, turning lanes, signal priority, queue jump lanes", amongst others, is a pre-approved Schedule A+ activity ('A+' signifying you have to tell everyone about it), so long as it is has no or minimal adverse environmental effects, at which point it would be a Schedule B activity.
So they can probably do what they need to do at Laurentian on the north side of Baseline from the Scouts Shop to beyond Clyde by way of the above. However, it looks like the bus lane extends east of the Scouts, possibly to the former IBM buildings at Merivale opposite Loblaws. They can use the same excuse as above to get from Merivale to Loblaws where there's a long right turn lane into the former IBM/current FedGov buildings - leaving them only the segment in front of the Scouts' buildings to have to come up with an 'A+' rationale for. Since it looks like they're going to consolidate the entrance to the Scouts and the Walmart into one (and remove the signalized pedestrian crossing in front of the former high school), they may just have enough of a rationale to get away with it.
One thing that gets me is what happens to the bus stops... since it looks like there will be separate right-turn lanes for much of the length of the project.
And of course the trees will most likely get the chop, be it directly or indirectly from having their roots cut up.
Btw, the City's list of required infrastructure projects in furtherance of the TMP includes the addition of bus lanes on Baseline from Richmond Road all the way to Heron and beyond to Walkley Rd:
Those still require EAs to be done.