The pro version has more features than the free one. Automatic navmesh calculation and layered grid graphs being the most obvious differences, but there are lots of other cool features as well as a few under the hood improvements. You can find a comparison page here. The list is large, but does not list every difference.

You can purchase the pro version in the Unity Asset Store. When you have purchased it, you will be able to download it in the Unity Asset Store, but you can also get access to beta versions by entering your invoice number on the download page. Beta versions contain new features and improvements which have not been released yet.

For simplicity, the license is the same one as the Unity Asset Store uses. Check the asset store for the exact specifications. It does allow for commercial usage.

Version 4 is a paid upgrade. Everyone who bought the package at most 8 months before the announcement of the release candidate (i.e after 2016-07-24) are eligable for a free upgrade and can simply continue to use their previous license keys. If you have bought the package earlier you can upgrade at a 50% discount. You can upgrade in the Unity Asset Store.

The Pro Version costs $100 (+VAT if applicable). It includes free upgrades to all future 4.x versions of the package.