How many chickens do you currently have? Is this your first adventure? Do you have an incubator? This is rather an intense breeding plan for two hens. I realize that eventually you will hatch out and have more pullets, but as a lady waiting for her first egg in a do over, it takes forever.
What do you mean by not going to pen breed? One really does not need a back up rooster if one only has two hens. Is this lady retiring? If so get MORE hens. If you start another line, you will need to separate them, or the dominant rooster will still be covering all the hens.
If she is not retiring, it would be better to get one rooster now, and then when you need to, go back to her and get a new rooster. If you get both roosters now, they will both be old at the same time. Multiple roosters are tricky to manage, the more roosters you have the more apt you are to have serious problems. If you are inexperienced, I would definitely wait on the second rooster.
I agree you are going to need to separate the rooster chicks out, they will need some protection from the elements. The pullets can grow up with the hens, be better for it.
Your intention to never bring in another outside bird is pretty unrealistic, unless you are incredibly lucky. In order to do serious breeding, one needs to hatch a great deal, and cull ruthlessly. Once you are on your own, your line will be influenced by her line, but over time will change. What breed are you working with? There is nothing wrong in getting fresh blood later on in fact it is a good idea. However, lines do not get depressed over a year, but rather years of breeding. You will really not need to start that other line for a couple of years.
I think she has put a lot of time into her flock, but once they leave her, they are your birds, and you are not honor bound to do it her way unless that works for you. Do not let her control your birds, but do go to her for advice, just know you don't have to take it, if it doesn't work for you and your set up. She is probably happy that she is establishing another flock somewhere else, in case something happens to her flock. All those genetics won't be lost. But flocks do change over time, keep in mind, that plans don't always work out.
Mrs K