If you already have a request for the novel then the query becomes something much different and many of my comments do not apply. The letter becomes more of a reminder of the story, a reminder of who you are, and thanking them for asking to see it. The query does not have the burden of what all queries try to do, get them to read a few pages and request more. Still, with a few changes, you have a strong query in my opinion and it doesn’t hurt to prepare for another go if you need it.
As for the similarities, your book sounds much different than In the Presence of Mine Enemies, and I put it out there just so you would be aware of it in case you get questioned by an agent (or editor in this case.)
To have a publisher interested is a very good position to be in and you should be very happy about that. I wish you luck with this, and don’t be tense about the letter (not that you need to be anyway), they are going to read the pages and that’s what counts.
If you enjoy alternate history, might I suggest Steven Barnes’ LION’S BLOOD. I was awed by his prose.