Domain Mapping Plugin: does it do anything that a .htaccess rewriterule cannot?

I'm running a Multisite set up to use subfolder structure and I need to provide domain mapping to each site for unique domain names, but I don't need to allow the blog owners to be able to set this up themselves.

So is there any advantage to using the Domain Mapping plugin instead of just setting up the domain on my host and using a .htaccess rewriterule? I had trouble getting the plugin working initially because one of the mapping options didn't work (a bug?), I eventually got it working but due to a limitation in the plugin I have to set up .htacess redirection for the other, secondary domain that needs to redirect to the first domain anyway. So I'm wondering if should cut the Domain Mapping plugin out of the picture altogether and just set up all domains using .htaccess.

What are the pros, cons and implications?