Yes and one more thing to add when selecting a Ground Control Station is that you’re probably better off with one of the “APM” variants over the 3DRobotics’s QGroundStation.
Support for Linux boards (i.e. Navio+ and another) is work in progress (but working) as you may have heard in the YouTube video from Randy Mackay shared here recently:
Because of the MAVLink “standard” all the ground control stations and devices should work together with any MAVLink software like a GCS. However it appears there are differences in newer settings and/or their behaviour, depending on which variant (original 3DR or APM spin-off). So for non-3DR devices or with APM compatible firmware (i.e. Navio), you’re best using one of the APM orientated solutions to ensure full GCS capabilities. Even then the developer of the GCS may lag behind the APM firmware, so some of the newest features may not be available for a while no matter which software you choose.
It’s even more confusing with the mobile software, because it’s not clear which variant the mobile developer was targeting when they wrote their software. What you can expect is core GPS location, tracking and telemetry communication with any software. But problems may occur when you try to select specific modes directly with the GCS (in my experience). At least you should always be able to use your transmitter to change flight modes for example, then use the GCS as a display/tracking tool.
This table sheds more light on the subject:
http://planner.ardupilot.com/wiki/other-project-and-common-topics/common-choosing-a-ground-station/
So the main differences on the APM side are for the mobile devices, but for the PC we only have two choices: “Mission Planner” or “APM Planner 2”. First of all I just wanted the latest and greatest, so looking at when they were last updated and some random comments scattered around the documentation it appears that APM Planner 2 should be a cross-platform replacement for Mission Planner. From what I gather of the history, MP was written first for Windows PCs as a Microsoft .NET solution. The other obvious clue was lack of updates, over a year, but that recently changed throwing the whole choice into confusion again.
What you will find comparing them is that Mission Planner is just nicer in some parts, that some features are just better there, e.g. joystick support. I’m still confused which one to choose and would like the guy who wrote Mission Planner to make a statement if he commits to future updates. This is the main reason I would suggest sticking with APM Planner 2, an open source solution is indeed the only sure way forwards. If you subscribe to updates of that you’ll see it’s buzzing with activity from dozens of developers and testers.