The city and the transit company should be working with the developer so that the new building has enough structural clearance for a future west train platform. With mutual cooperation, the developer should be allowed to add a few more floors to their tower.
In the case of the Main_Street-Science_World_station, the VanCity Centre was built at and over the west side of the station.
https://www.mcmparchitects.com/projects/vancity-centre Aside from the building not even reaching 20 floors, its a fine example of being built over the train structure.
https://sfuurban.wordpress.com/2012/07/24/main-street-skytrain-station-the-history-part-1
https://www.translink.ca/about-us/doing-business-with-translink/real-estate
https://fcr.ca/properties/british-columbia/vancouver/new-westminster/shops-at-new-west
https://en.wikipedia.org/wiki/New_Westminster_station , https://en.wikipedia.org/wiki/Shops_at_New_West , https://www.shopsatnewwest.com
https://www.loopnet.ca/Listing/800-Carnarvon-St-New-Westminster-BC/29986774/