Let me use my pen as a mouse setting --- utility for this? Or way to enable per app?

Okay, it turns out that while this option allows Macromedia Freehand to run, it disables certain other apps.

Is there an easy way to enable/disable it?

Or better still, a way to enable/disable it for specific apps when they run?

EDIT: Or, is there a way to exempt an application from this setting when it is programmed? (The specific app I need it for is an opensource app programmed using Godot, OpenSCAD Graph Editor)