Yep, you can open the workflow and edit the Run Script element. Right at the top there's 2 lines that say
var alfredLightTheme = "Alfred"
var alfredDarkTheme = "Alfred Dark"
You can change them to whatever theme you want for when the mac is in light/dark mode. Just put them both to the same theme name if you want it to always be the same.
I may be adding support for other apps and I'll make the process better if I do.