Agree with manual explode, in general.
When doing a manual explode, BE SURE to use the "Triad" tool, which allows you to move a part ONLY along one selected axis that you can choose.
If you do not do that, you may find that what looks like a simple move of left or right has also moved your part away from you by some unknown distance. That is not such a big problem if you are already in the view orientation you will want, but if you have that happen and try to change viewing angle, the exploded view may become very messed up.
The issue of the boss and bracket is essentially an illustration of the drawbacks of "quick and dirty solutions". You are best off to change the part to reflect the real configuration, or these things come up. GMD makes it so easy to change , that I do not see why you cannot just make the change in the part.