You'd like to identify an interference between two parts. In addition, once identified you'd like to subtract the one part from the other and then add some tolerance to the subtracted feature.
You can use the Analyze Interference tool to find interference.
When you analyze interference, the tool seems to require you to define 2 selection sets, but you can create just one. If you add components to both sets, all of the components in selection set 1 are checked against all of the components in selection set 2. But if you do this Inventor will not report any interference between components within the same set. This can actually be very helpful when you want to ignore known interferences (such as press fits), but check those components against others.
With all of that in mind, I can tell you that I almost never define a set 2, instead I just add everything to set 1 and then click OK. With just one selection set, Inventor checks for interference among all of the selected components.
Once identified edit the part to subtract from, while in the assembly. Then use the Copy Object tool to select the interfering part and set the Create New option to be a surface. Note the Associative checkbox indicating that the resulting Copy Object surface will be Adaptive. Therefore, changes to the copied part will update if/when the part updates.
Here you can see the results of the Copy Object.
Next you can use the Sculpt tool to convert the surface to a new solid.
Here you can see the results of the Sculpt tool.
Next use the Combine tool to subtract one solid from the other.
And finally, use the Thicken/Offset tool to subtract-offset the resulting feature faces with a tolerance as required.
Keep in mind that it is always a good idea to toggle the adaptive status of a part to be off once that part is at a "stable" design point. If you need to make changes that involve the adaptive feature again, you can toggle the adaptive option back on.
Additionally, here is a Youtube video I made on this subject a while back that shows a shaft being subtracted from a foam insert: