@Carson Jones
As this is a script, Adobe can't really add a checkbox into Preferences, things don't work that way. Adobe could add a checkbox to the script interface though. I have added my vote.
To achieve the desired result without waiting for Adobe to possibly implement this you can edit one line of code.
The Presets/Scripts/Load Files into Stack.jsx uses support scripts.
Edit with caution:
Presets/Scripts/Stack Scripts Only/CreateImageStack.jsx
Change line #371 from:
app.activeD
...