I'm not convinced that the Harbor Blvd crosswalk is going away. There's no access directly from Harbor Blvd to the pedestrian bridge, which makes me think that the existing crossing will remain for people coming from the hotels.
There is still a wide walkway entrance with a gate near the existing crosswalk (circled in red, below). I suspect that this will be the main pedestrian entrance. Additionally the "Disney Shuttle Drop-Off" will presumably be the Toy Story buses, which will also need security screening (access circled in blue)
With projects like this, it's not unusual to break things down into smaller individual project to specialize, or to not show a certain discipline on a plan for clarity. I don't see any meaningful road work on Harbor Blvd (other than removing the existing passenger drop-off entrances), so if any work is to be done, it would be under a separate project
Similarly, the work done in the existing bus drop-off area is a separate project that isn't being shown here. I suspect some of that space may get annexed by DCA, but there will also be a security facility there, along with a path connecting the Toy Story drop-off (and Harbor pedestrian crossing?) to the Esplanade
At Disney Way there are lines that appear to be a crosswalk at fist glance (circled in yellow), but they extend onto the sidewalk on the west side of the street and turn downward; I suspect this is actually the easement for the Edison power lines. I bet the existing crosswalk here will remain (similar to the crosswalk near the existing bus plaza), but the lines shown on the plan are for something else
As an aside, I hope that they also move the security on the west side to put all of DTD and the M&F tram inside the clean zone, to allow free-flow through the Esplanade again
As an engineer who regularly designs transit facilities that are quite similar to this (though more utilitarian), I'm totally geeking out right now! And if anybody wants a good laugh, go check out Martha Schwartz's description of the original design intent (click on the Details button on the left to find it); it's a perfect example of all the things that went wrong in the DCA1.0 era:
http://www.marthaschwartz.com/disneyland-east-esplanade-anaheim-ca-usa/#