I too had difficulties making the adjustment, but I now much prefer that another process, albeit programtically, manage this.
Why do you need a procedure to keep track of unique naming if there's a surefire method in place? And if the CEO wants a report called Dashboard, and the Network Manager wants one called Dashboard, why should I care that they use the same name? I do gently suggest that they further qualify it, but it doesn't really matter to me now.
As for people overwriting a report, that can happen regardless of the naming. To address your concern, I do NOT allow developers to publish reports into CE production folders, that is handled by the Crystal Administrator.
Developers push reports into Test/QA, when they're signed off, the Crystal Admin moves them into production.
I also do NOT use CE as my report repository, I use VSS, etc., as most would do for code.
A little obfuscation might be a good thing here, rather than giving the developers an opportunity to directly get at the reports in their folders, I would prefer that they use the provided tools to do so.
So red flag or no, it should provide a simpler and safer means to manage your reporting infrastructure.
It didn't sit well with my command line origin (Unix and DOS), but I find it oddly comforting now.
-k