Well, establishing custody for the NOW doesn't have to mean you are done with the R. The marriage and custody are two separate issues.
The time you have with your children isn't about the marriage (or not) - it's about creating the best possible scenario for you and the children. If things change between the two of you that is great! If not, well, you have created framework for your new family (you and the children).
Plus - if she did want to get back together and you decided to take her back lots of stuff would have to happen and it won't happen overnight. In the meantime no reason you can't keep building for you!
"What is best for my kids is best for me" Amor Fati Link to quotes: https://www.divorcebusting.com/forums/ubbthreads.php?ubb=showflat&Number=2879712