it is a five year visa. There are already people trying to scam the requirements. Regulations will be put in place to address those loopholes. Grandfathered in means you come under the rules and regulations in place when you first received it, not regulations added in the future.
You can not extend your entry stamp in Bangkok until you have 45 days, or less left on your entry stamp. Other locations in the country require less than 30 days, and a few locations require that you have less than 7 days left. You can not immediately extend your entry.
immigration has all your entry, and exit details. They also don't start processing your application immediately when you apply. If your immigration exit stamp shows you left Vietnam before they started processing your application when it came up in the queue, you better return immediately and send them proof you are there, or the rejection can be expensive. They asked for proof you are in Vietnam. What happened to others has absolutely no relation to your case at all. You can't argue with them. If you don't return, and your immigration entry stamp shows it, no matter what you say, they will reject you. They do verify your location by your entry, and exit notations in the computer. They know exactly when, and where, you entered, and exited the country, as it is all in the immigration computer system, and for every country you've entered and exited.