Oddly enough, about 2 weeks ago, I came up with what amounts to be the same technique, including the multiple vss subprojects and a single working folder.
I did note that if I check a file out of vss (e.g. dbo.tablex.TAB) , edit it and run it in query analyzer, and then check the file back in, then I get an odd issue that the version that sql server holds differs from the vss version in that the sql version somehow adds extra line breaks...
Anyway, like you, I have several developers who don't always use vss, but go straight to enterprise manager. So every few days, I generate the sql scripts for the entire db to my working folder and I run a recursive differences report on the entire vss project. This allows me to catch and persecute the offenders very quickly.
I am actually thinking of writing a job to automate the generation of the sql scripts and reference vss object model to create the differences report and then email me info. If it is cool, I will post the code.