Faculty members who read this forum have consistently pointed out that a good GPA in a graduate program significantly alleviates the concerns regarding low undergrad GPAs, if not eliminates them completely. There are also numerous examples of people who got into some of the best programs in the country with undergrad GPAs similar to, and even lower than, yours. The algorithm issue may or may not be correct, I do not know. Even if it is, given what we have been told by the faculty who has ad-com experience at the top schools, including at CHYMPS departments (such an ugly acronym, this is), this should not be something to worry about too much based on your MA performance.
Again, I am just trying to say that there is no need for someone with your profile to shy away from applying to top schools - not that you should apply exclusively to them. Applying broadly is a good strategy.
Regarding the email issue, I can't see that it will have an impact on anything. I can imagine the reply will something like - "We encourage you to apply. Committee evaluates the application materials as a whole, so weaknesses in one part of the application can be compensated by the strengths in other parts etc.." You can still try though