It shouldn't. Apache keeps running during the upgrade process normally as expected. At the end of the upgrade is when you apply the changes and Apache Restarts with the new setup.
What about old configurations? Does rebuiling apache, overwrite previous settings of apache and php? if yes, what settings? extensions? patches?****...
The first message/option that is checked you should see on the EA3 page is this:
Previously Saved Config (** DEFAULT **) [Hide Info]
↑ This option loads the last saved configuration. If the configuration is missing, then default values will be provided.
Below that you see a button to "Start Customizing Based on that Profile"