"In fact the plug in seems to pretty much automate the manual process as detailed here."
It looks like it does, but if you actually read the plugin code, it doesn't.
also, if you have sub-blogs off the main blog, and also Sites, the ID numbers are off. The will be off for Sites by as many sub-blogs you have on the main site. Say I have three sub-blogs off the main install and a few sites. The Site ID will show as 12 in the backend, but will actually be 15 in the database.
It also entirely gets rid of the blog's Edit page.
"But having read his own comments (as well as those of users), this really isn't ready for release on a production server yet and there are still some fairly significant missing features."
??? News to me. I have it running on production servers just fine. The "significant" missing features is probably referencing the whole "it's not exactly like wp.com!" which it will never be, because parts of that they aren't releasing.
Donncha's plugon maps domains just fine. haven't had an error or issue with it yet. It's slim and lightweight. if you want to have sub-blogs use their own domain, this is the one to use.
The only up side to the MSM plugin is if you want one of those sub-blogs with a mapped domain to have the ability to have sub-blogs off of them.