Hi Jeff.
you asked, "One quick question to help guide us: When you make this hole do you expect it to affect the linked component itself? That is: if you add other instances of that component, do you expect that hole to appear in all instances? ".
Yes, that would be great. Total fluidity. If you want to protect an instance of a file, then the user should just make a copy with a different name. Then this would not be effected by a higher level change or any change to that first instance's file name. You could make it selectable in the user's preferences.
Then you continued, "or is this hole more of what we call an "assembly feature", meaning that it only affects one instance of the component?"
Again, make it selectable for all projects in the user preferences if you like. So, the thing is, sometimes it is only at the assembly level that you can make holes (as an example) relative to other components. In my case it was about making holes, for screws, that would hold together 2 components that are positioned in space relative to each other until the screws are installed. So the holes needed for this are more easily made when the two parts are in place.
Now, since my post I figured out a work-around. That was to break the links of part A and Part B from their original file, and the make the holes. After this, I exported each part again and relinked them to the top level assembly file. In my case, the two parts were of different shapes and sizes so to make a measurement from a single point, like the bottom edges, very tough. I mean, if I make a change to the base file then it is inherited by the top level assembly file. Why not make it work both ways. So, you are a programmer and you know that this is not how OO works in C++ for example. You are right, but that is different in that you are not screwing classes together at a higher level. Well, you could if you made a class that used a couple of subclasses within it. (This is starting to sound like a college sociology class)
This is the long way around the barn and I would suggest that you not make this the rule in your finished product... which you expect people to pay some $15k for.
I would think you would want to follow, at least to some extent, how people think when building things by hand. If you would like to see what I am talking about I could send you a file, but only in an email not to be published. There is an autodesk person that I do that with. He understand he is not to show anyone my work.
By the way, my install has been crashing a lot lately, mostly when moving from work online to work offline and back again. I find it much faster to work offline, then to update my online account once in awhile.
Jim