You are right that there is currently no way to add custom annotations to the Edit > Insert > Transition List table. However, you should still be able to paste most of what you want into that table and then finish by pasting into the Document Grid, using a saved report template like a modified version of "Small Molecule Transition List". You need Edit > Insert > Transition List to create new targets in your document, but once you have those, you can further annotate them with the Document Grid. Furthermore, if you are worried about ordering, you can use a sort both in the Document Grid and in, say, Excel to make sure the values you have line up exactly with the rows you are pasting into in the Document Grid.
Hope this makes sense and allows you to achieve the annotations you want. It is unlikely that we can add custom annotations to Edit > Insert > Transitions quickly enough to satisfy your current need. So, this two-part solution is about all I can offer you. It should work, though.