So, this brings up a question - if you legally canoed the Rio Grande and filled out all of the customs paperwork, then when asked if you crossed into Mexico, I guess the "correct" answer would be yes, I inadvertently crossed into Mexico while canoing the Rio Grande...

There's no 'inadvertent' about it. This is great disconnect in the border policy. Remember, when you are prevented from crossing for tacos you don't get to eat. If they applied the same process to boating they would put all the rafting companies out of business. It's not about security, it's about money. I have long advocated that if I cannot cross the river, then boaters cannot either...too bad about their business, find another. It's a double standard and it isn't right. Try getting any official to address that....good luck.
BTW, you don't fill out Customs paperwork to run the river. It is just accepted that everything is okay and because you have a river permit you are good to go. The NPS and Customs and the BP all know you cannot stay on the north half of the water.
So, if I get a permit I can stop and even camp on the Mexican side with no fear of enforcement. But if I go to Boquillas I have committed a security breach so serious that jail could result. Give me a break.