Boyd, right now the design updates do allow for custom text modification types where you can pass it which description to use for that type of modification. This is a new feature that isn't available in SE4. I think that will handle 90+% of people. I have some ideas for handling total per-transaction description customization but I'll keep that a low priority item for now since most people probably won't care.
Wesner, I believe what happens (in SE4 at least) is that it will locate the first indicator that is affected by the modification via binary search. Then it will remove or resize the appropriate indicators. What you would want to do is track which indicators are removed, and store those in custom undo data. Then later on when an undo occurs, read the custom undo data to see which indicators to restore. Of course this assumes that we provide a way for you to read/write custom undo data.