Go to the addon file location:
Copy the py file to desktop or other place.
Open with Notepad or other editor
Find the text: def boolean_mod
Add text between line 580575 and 581576
md.solver = 'FAST'
Save and replace the original
It will use the fast algorithm when apply the modifiers in this operator.
But may be it cannot improve the performance because blender use exact solver on default when create a boolean modifier.