Reasons: citizenship is for sale through the Quebec Immigrant Investor Program[2] so if you're wealthy, you can effectively bypass this tax. If you can't, using a relative as a proxy buyer will let you bypass the tax.
And preventing non-permanent residents from buying means any immigrants who come to Canada but aren't PRs will pay this tax. These seem like the exact kind of people you don't want to disincentivize from buying - people who are willing to take a risk to come to Vancouver, but aren't rich enough to just buy their way in.
Taxing people based on where they file their taxes makes a lot more sense to me - if you're paying taxes in Canada, you're not using Vancouver housing strictly as an asset class which is what should be discouraged in order to have a healthy, diverse city of people who own where they live.
1- http://www.theprovince.com/business/proposed+could+high+cost...
2- http://www.immigration-quebec.gouv.qc.ca/en/immigrate-settle...