I do kind of understand they don't want to commit to "yes we will make it better" if it turns out to be an engineering nightmare to actually do so. But I do agree that what has been proposed is far from ideal and any reasonable opportunity to do better should be taken.
Also the stations are not going to be shallower, regardless of whatever method they use to move people between platforms. There is simply too much built around Queen St in this area to go any shallower without it interfering with building foundations, the existing subways tunnels, etc. All of which would require a massive increase in cost to deal with, which lets be real, makes that a non-starter. The best we can hope for is fewer separate sets of stairs and escalators, or ideally, multiple high speed elevators.