I'll just throw a little thought in here between boinc installations on windows and linux.

Of course you all know that when boinc installs on windows, you get the registry entries, and you are pretty much limited to one main boinc installation again due to the registry entries unless you are one real hard core windows internal code guy/gal.

On linux though you can install boinc as many times as you want. Each BOINC directury just needs to be a sub directory of another directory in the users "home" directory such as;
/home/sum_dude/boinc_1/BOINC for the first for instance,
/home/sum_dude/boinc_2/BOINC and so on ad-nauseum

And why do that? Well it solves a problem of having to worry about whether or not you can change projects you are working on. ie not having to do what the "scheduler" says. Of course this isn't the way that the windows boinc world runs. But it sure makes it very simple to run multiple instances of boinc working on different projects at the same time on dual core systems, or on single projects where the owner just wants to crunch on boinc projects under his/her own time tables.

Why mention this? Because I'm sure that others have thought of this too, but in the process the "cross project ID" issue looms up and needs to be looked at.

So I would imagine that to the boinc authors in their grand scheme of things prefer the windows registry method as it gives them the total control over the system. With *nix, you don't get any total control unless you are "root".