Hey Dan,
The new component we're using is completely different from the old one we used, which dated back well before Toad 9.6. It should be doing a much better job at lining up matches and mismatches in code. In fact, when I took a look at most of the currently-available Windows comparison tools out there, the only one I could find that had this kind of functionality was BeyondCompare.
Do you have any examples that you're running into where it's not matching them up well enough to help illustrate the scenarios you mentioned? The reason I ask is because most of the current tool sets for file comparisons should be doing a well enough job where a manual override or linking shouldn't really be necessary. The first two examples you provided should be recognized and handled easily with the new component. I can definitely understand the theory of how manual linking could potentially be beneficial, but I'm looking for real examples to help drive the argument to add it.
The third example you provided may be addressed in one of the updates I'm hoping to make for this release. The merge window will already give you the option to use lines from the LHS and RHS of the compare window (through the tool buttons or clicking the diamonds next to each line). You can also manually copy and paste items from the LHS and RHS into the editor at the bottom. However, I'm hoping to expand upon this functionality a bit more for this coming release.
Having some real-life examples that you're running into would be very helpful in making some of these enhancements.
-John