Is there a way to use interference checks to determine what material needs to be subtracted away from other parts to get the clearance needed? (See Attached) The way I typically handle this is to project the lines from one part onto the sketch of another and proceed accordingly, however as you can see, it didn't work out well in this instance as the face of the part in question is not parallel with the sketch plane in the other..Therefore making the cut location inaccurate.
If you edit the part to be cut in context of the assembly (rather than open the part file and editing it separately), you can use the Copy Object tool to copy the other part into your part as a new Solid body. Then you can use the Combine tool to subtract the one from the other.
Alternately, you can use the Copy Object tool to copy the other part in as a Composite surface and then use the Sculpt tool to subtract it from the original part, and this will create an adaptive link, so that if you make changes to the one part the cut will update.