I don't see a need to modify Elve at this point. It's a external hardware issue that's easily managed at the source. It simply that the Pronto has too much IR output for the nose to nose method of learning. Give it a foot of separation and no problem.
Not surprising, the Pronto is known for having the highest output on the market.
If users are getting incorrect frequencies with their specific remote, the first thing to try is backing away a little.