When intersecting two bodies, the Target Body is always cut. This works great when that's your goal but sometimes I want to keep the target body intact after the intersect command. Keep Tools does not do this.
The only work around is to reverse my selection order from Target Body and Tool Bodies and then do another cut command after.
An example is to make a form fitted lid over a target body. Placing another body intersecting the Target Body, then selecting intersect should have an extra check box that states "Keep Target Body intact". This would not perform the typical intersect command and instead.