You could create a gui with buttons and then use timer commands to make it always float over the same part of the underlying application. For example, the button could always float to the right of the text "calculator" in the calc.exe titlebar. The button might lag behind a little if you drag the window though.
Another alternative: If the application has controls that AHK can operate on then you can likely also relabel and reuse buttons from the GUI. Start calc.exe and then run this test code. It hides the "sinh" button, relabels "cosh" to ":-)" and takes control over what action to do when you click ":-)", for example show the text "hello world" in a tooltip. edit: though this disables click+drag within the calc window. A better alternative might be to use middle mouse button ( Mbutton ) since click + drag is less commonly used. Then you can keep the native left click functionality of the button.
Control, Hide,,Button37, ahk_class CalcFrame
ControlSetText, Button38,:-), ahk_class CalcFrame
#IfWinActive, ahk_class CalcFrame
WinGet, x, ID, ahk_class CalcFrame
MouseGetPos,,, xwin, xcontrol
if ( x == xwin AND xcontrol = "Button38")
ToolTip, hello world