And basically the strange artifact is a result of the booleans not getting a full closed intersection curve at the juncture point.

If you look at the weird result on the main body you'll see that there are some places where there are not any edges, like here:



So the edges that you do see there are sort of more like little infinitely thin slits cutting the surface, rather than it having a full closed boundary making a proper hole there. Probably your side surface is just very slightly hanging to the outside of the main body in those particular areas.

If you move it over just a little bit so it pushes through, it will help make the 2 surfaces have a cleaner intersection between them - that's basically why having things push through each other a little bit instead of skimming can help.

- Michael