I'm not worried about this. Peak point ridership will be low because of an abundance of transfer points: Mt Dennis, Eglinton West, Yonge, Don Mills (DRL) and Kennedy.
But we're still not certain of the actual details of RER, especially under this government. The east section may not be that much of a concern, but the west side definitely is. Those traveling downtown would transfer at Mt Dennis and not Caledonia, so there's truly only one transfer point between Pearson and Eglinton West. Even so, at both station's I'd argue that the net influx of riders to the crosstown would be equal to or greater to those that choose to transfer to RER. Remember, Eglinton is a huge employment corridor in the city.
While the abundance of transfer points is great and honestly should be expanded on other rapid transit lines in the city, I don't believe the city should consider unbuilt transfer stations in their traffic studies (when considering loss of riders, gain of riders should be considered for planning the long term viability of the project), especially when the opening date, actual capacity, success, etc of those new stations/lines are completely unknown. I see issues with most if not all of the transfer points on the line that might make them unattractive to users:
Mt. Dennis: Service onto the already overcrowded Kitchener line, and the soon to be overcrowded UPX. It's also a GO station and we don't have the fare integration information necessary to give precise traffic estimates
Caledonia: Same issues as Mt. Dennis, only there are far fewer options for travel along that line — You're either going to Union or north, which I doubt most people are. If you're going to York U, you'd probably be more inclined to transfer at Eglinton west due to ease of transfers, and the fact that you would not need to transfer a second time at downsview park
Eglinton West: Large influx of traffic at the station.
Eglinton-Yonge: Crowding on the Yonge line
Science Centre: We don't really know when or if RLN will be built, and we don't know if and how many people from York Mills Rd, Lawrence Ave, and Sheppard Avenue will transfer from the relief line to the crosstown. If it takes till 2041 to built (the best case scenario), then the crosstown will have been running for 20 years, of which, a lot of development would ensue on the corridor, making it more attractive to businesses not willing to locate downtown
Kennedy: This one is interesting. Again, there are issues with GO, but there's also the crowding issues that will inevitably ensue on the Danforth line. I honestly see a lot of people that currently take Line 2 switching over to Line 5, making it more busy than it would have initially been.
Of course, this is all speculative, but the point is that there's a huge amount of uncertainty with regards to the viability of all these transfer stations. It'll be interesting to see what ends up happening and whether capacity will inevitably be an issue for the line.