You can work around this by schema comparing your development database, rather than the project, to the live database. Keep in mind that you would have to deploy the project to your development database first.
FYI - The fact that the variables are not substituted is only a problem in the comparison window. The variables do not cause false differences during the comparison (in other words, Schema Compare does substitute the variables when comparing) and the variables are substituted when you update the target database.