1) Yes, remote agents work from the VTune Analyzer for Linux GUI. The remote agent works from Linux to Linux and from Windows toa Linux system. We don't have the Windows remote agent supporting Windows to Windows anymore. No you don't need a seperate a license.
2) The sample-over-time will work in the upcoming VTune Analyzer 9.1 for Linux product.
3) Currently we don't have any plans to support counter monitor on Linux.
I hope these answers your questions.