The Valley Line West crosses one (1) stop light going over the Henday. the tracks run parallel to 87th Ave, which has signalized entrances and exits onto the Henday, in the form of T intersections. the tracks are on the south side of the road, meaning they only block one of these exits. i'm not sure what the issue with that is. the exit already has traffic lights on it with a long cycle, the train would only block a couple turning movements that are already controlled by lights; the train is going to have a minimal impact on that intersection, and be moving waayyyy more people than the cars potentially stopped at the traffic light. given the relatively small scale of 87 Ave, that it's mostly for commuters as opposed to industrial traffic, and that the train would only mean an adjustment to a signal already there, I think it makes sense.
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I wouldn't put too much store by St Albert's 'plan' as shared here. it's literally a line on a map, from a few years ago. it doesn't accurately reflect the Campbell station as shown in CoE's more recent documents, which hints to the design just being conceptual. The fact that the line they show goes through the interchange rather than around it is probably just for clarity's sake.
For what it's worth, I'm betting the line gets elevated over the whole interchange, as 216 is a major freight corridor and has minimum clearance requirements, which i would assume also apply to its approaches, but that's a bit of engineering that would make more sense to resolve a bit later, closer to the line actually being built.
It's also a train that, at full buildout into St Albert, already be carrying hundreds of people across that interchange during rush hour. slowing down a light cycle to accommodate that, even potentially at the expense of a dozen or two people in cars, is a pretty fair choice to make i think.