just different brands. I wouldn't worry about it.

I can't give you an absolute "yes" because you never know what else might be out there, but in most cases I think you'll be able to. The USB controllers will probably just show up as a joystick/game controller and most sims will let you set it up as your controller.

RealFlight comes with it's own controller so you don't have to worry about it if you don't want to. The controller also acts as a copy protection dongle so it always has to be connected when using the program, even if you use another controller. It comes with cables to connect your own TX through the controller if you want to use your TX instead, or you can select any other joystick/controller you have connected to your computer.

Phoenix looks like it comes with a USB adapter that will let you connect any JR or Spektrum radio if you already have one. Horizon Hobby also has a package that includes a Spektrum DX5e TX for $45 more.

I think Clear View should work with just about anything that you can connect through USB, including the dedicated controllers you linked earlier or a real TX connected with a USB adapter (you can find adapters all over) it just might require a little more setup to get them talking to each other. The Clear View website actually recommends the 4ch esky controller "for best results". You can find a bunch of adapters here: http://www.allerc.com/index.php?cPath=91