Hello, the second appearance of Configuration wizard is a known bug, which was decided to fix later to release the HF as soon as possible. The Hotfixes are done the way, so they aren't removed by CW or by repair.
Ad upgrade of module question: The hotfixes are targeted for Orion Platform 2015.1.2, which is the latest released so far. If you upgrade some module, e.g. SAM, this won't touch the Orion Platform installation and will just install your module. Reapply won't be necessary then. In future, when new version of platform will be released, the HotFixes will be removed by installation and you'll get brand new installation of the platform.
I hope it helped.
In my case, running the hotfix installer ended with a prompt to restart the server and run configuration wizard. I wasn't sure whether I should postpone the restart or run the configuration wizard first. I opted with a restart first, thinking configuration wizard would start automatically again upon startup but it didn't.