Firstly, "will get them to Union quicker"--what percentage of users boarding from VMC, 407, Pioneer, York, and Finch W are likely going to Union? If they're going to any station whatsoever other than Union, and that includes any surface/PATH point north of Union or any destinations along the 509/510, the subway would certainly be faster due to not having to walk from the GO train at Union through the station to get back to the TTC station to continue their subway trip (not to mention paying a double TTC fare, on top of the existing TTC/YRT subway and GO train fares!) or to walk north/into the PATH.
Secondly, I don't agree that it would necessarily be faster even heading to Union specifically. This hypothetical rider would be sitting nicely in their seat on the subway, and would have to exit at Downsview Park, go up to concourse level, tap out, go up to the southbound GO side of ground level, tap on, and walk out to the platform, then wait an average 7.5 minutes (0-15 minute range, if on schedule, that being for RER once it goes live in 7 years if we're very very lucky) for a train and have a ~15 minute ride to Union. That compared to staying in their seat and taking a ~30-minute trip to Union. Would GO be faster, all that considered? Also, this rider would have to pay an additional $5.02 GO fare (current Adult Presto fare from York U to Union) on top of the $3.50 YRT+$3.00 TTC fares they'd already paid to travel from VMC to Downsview Park, for a total of $11.52 vs $6.50 for the whole trip--not to mention the likely fare increases to come by then. They'll pay approximately 1.75X as much for a TTC+GO trip vs a TTC trip alone, assuming fares increase in a relatively proportional manner.