Well, it depends upon the changes. If you are thinking your dot files (ie .bashrc, .vim, or /etc/bashrc) they will all be the same after an update as they were before. To pin your commit, is intended to give you a reliable known state to boot, usually this is done with all layers intending to capture everything the way you have it. For that you use
sudo ostree admin status first to get a list of deployments. Then you use
sudo ostree admin pin <deploymeny-ID> to pin the particular deployment desired. The default deployment number is usually the first, which is number 0. Earlier deployments are 1, then 2, etc… You can also tell ostree to keep more than two commits all the time outside of the pinned deployment. I suggest you read the docs for rpm-ostree and read the docs for ostree as well.
So in short, if what you change on your system is aliases in /etc, and /etc/bashrc or in ~/.bashrc or .vim, etc… no fear it will be there after reboot. Flatpak apps are also not affected by the rpm-ostree beyond the actual flatpak tooling and runtime, which normally don’t affect the user.