Sorry for the delay.
The reason for having the option to not include dependencies is basically so users can choose that unselected objects are not brought back into the project under any circumstances.
If you need the tool to help bring any connected objects back into the project, then that's when the 'include dependencies' option should be used. If it's performing dangerous or undesirable actions, then that's the issue we need to look into.
A lot had changed in the tools dependency engine in the last few years, so you might find it reliable now.