These situations do exist, but that doesn't change the point that the genie is out of the bottle. People who want this software are going to be able to have it

These situations do exist, but that doesn't change the point that the genie is out of the bottle. People who want this software are going to be able to have it. End of story. If a timing attack happens to pop up in it, great, that's a win for the government. But by and large, these messages will go without decryption. As with anything: these measures will not stop the determined lawbreaker - not that they necessarily need to.