It sounds like Installatron will be able to assist you. To answer your questions:
The Installatron import process will not modify the installation in any way. Installatron simply scans the install to learn more about it, and this information is recorded in an Installatron data file for the installation.
Any customizations to PHP files will likely be lost by the upgrade process. This isn't an Installatron limitation; the Mediawiki upgrade process replaces old Mediawiki files with new files. Other customizations, such as Mediawiki settings or extensions, should not be affected by the upgrade process, however we strongly recommend confirming extension compatibility with the new version prior to attempting an upgrade.
We always recommend creating a backup prior to any upgrade. If any issues arise, the backup should be able to be restored.