1. SSIS can be installed seperately from SQL Server. You basically ONL choose SSIS when you do the install.
2. Licensing is STEEP, SSIS is NOT licensed seperately, you are basically burning a FULL sql license to install SSIS (or SSAS or SSRS, etc.) all by itself.
3. This basically limits you to using the file system to store packages unless you configure it to look at a SQL Server elsewhere where packages could be stored.
I have some experience with this config and have typically installed a SQL instance as well to support SSIS and do scheduling of packages locally. No non-system databases were installed.
This config is more typical with large organizations trying to limit where ETL is happening and get better visibility. I haven't seen many small organizations do it because of the cost.