They are called applications because that is how most people will use them; to define actions which only happen for one program.
However, an application is really just a set of qualifiers to identify the window where the gesture began and whether it meets the specified criteria. For example, you could define an application which matches any web browser, or only when over a certain control class name regardless of what application it is in.
When you first press a stroke button, StrokesPlus.net examines the control directly below the mouse. The first thing that happens is it checks to see if this belongs to an ignored window, and if so it stops processing and lets the stroke button event pass through. If it is not an ignored window, it stores the control and main window handles which will be passed into the action script if a gesture match is found.
See Defining an Application for more details.