This is an old question, but I thought I'd answer it anyway.
There are numerous differences between the two products in how features are presented, but they have near feature parity (there are actually many things Virtualmin+Webmin can do that cPanel cannot do, but they would rarely impact someone primarily managing websites, I'm not aware of anything cPanel/whm can do that Virtualmin+Webmin cannot do).
Virtualmin Professional includes a feature called "Install Scripts" which provides installation of 100+ web applications, similar to the tools you've mentioned. So, I don't think this can be considered a limitation of Virtualmin (though Virtualmin GPL only includes a very small number of Install Scripts, so if you're comparing free Virtualmin to paid-for cPanel plus paid for Fantastico, Virtualmin would not compare as favorably).
Here is a list of Install Scripts currently included in Virtualmin Professional: http://www.virtualmin.com/documentation/install-scripts
New scripts are added periodically, as users request them, and if they are reasonably easy and secure to deploy in a shared hosting environment.
I made a comparison table many years ago, which is kinda out of date at the moment, as it's missing much discussion of a lot of more modern features that have been added to Virtualmin and probably cPanel (stuff like node.js support, cloud service backup options, nginx support, etc.). But, I believe it is still accurate for the features it does cover.
Disclaimer: I'm a developer on Virtualmin and work for Virtualmin, Inc.