Hello Nikolay and welcome to our forums,
First of all, please accept my apologies for the quite delayed reply.
Regarding the RunOnce key, this is usually used for when a prerequisite requires a restart, so the main setup is relaunched after the restart to finish the installation (e.g. the installation of a second prerequisite).
Just noticed when using /passive switch in MSI command line (bundle.aip -> Builds -> MS command line -> /L*V "[WindowsVolume][|ProductName]-[|ProductVersion].log" /passive) the issue is not reproduced but bundle installer as expected is running without UI.
This most likely happens because when the main package is launched with no UI, the feature-based prerequisites are installed after the main installation (similar to post-install prerequisites).
Now, I have tested the sample project you have sent me and I was not able to reproduce the behavior you described. I have tested this on my VM, multiple times by reverting the VM and it never occured (out of like 5 times).
Are you able to constantly reproduce this, or it rarely occurs?