Strictly from a money perspective it doesn't make sense, but there other advantages. Going on SP's rough diagram, the buildings built in place of the surface parking could generate as much as 2,000 residential units. The property taxes from those units should easily offset the cost of maintaining the newly built parkade, and even the upfront capital costs. It also means another 2,000-3000 people have walking access to a train station.In summary - could we build a replacement parkade? Sure we could. It's just a really, really inefficient and expensive way to produce the same amount of parking than if we just got rid of 48% of it right now and not build anything else.
Personally, I would okay with the city doing away with all parking and developing all of the space, but I also think having a small amount of parking gives some flexibility to the system. It's important to remember that the transit system as a whole is subsidized, and if it only existed on whether it made financial sense, there wouldn't be a transit system. I'd rather see a parkade built then leave empty surface parking land undeveloped.
IMO, the 510 stall parkade is a reasonable compromise. It adds an option for some people who need to use the station, but find the bus feeder system isn't a feasible option - and from my own personal experience this can absolutely be the case. Whether we charge or not, is another debate. I would prefer to charge, even it's a couple of bucks.