Some stuff can only be done through bpy.ops, like changing the order of modifiers (if you really didn't want to use bpy.ops, you would need to remove all modifi

Some stuff can only be done through bpy.ops, like changing the order of modifiers (if you really didn't want to use bpy.ops, you would need to remove all modifiers and recreate them, though this would severe any references to the old modifiers outside of your script, so you really can't do it without bpy.ops). Also sometimes operators are faster, so resigning from them sacrifices performance. And of course sometimes there just isn't an equivalent non-operator function, so you would need to recreate a functionality in order to not use an operator.