You can write your own merge drivers, or write a set of clean and smudge filters, so that Git doesn't do this merge, or doesn't see this line. But in general, no, there is no simple way to do what you are suggesting.
As a general rule, any sort of "configuration" data should not be committed to the source repository itself. Instead, if it's appropriate, the source repository should contain a sample configuration, and the actual configuration is kept elsewhere (either .gitignore
-d, or outside of the work-tree entirely).
If configurations need to be upgraded when the user goes from "FooBarix Version 1.3" to "FooBarix Version 2.0", the 2.0 version should probably include a configuration-migration program that gets run during the upgrade, saving the original configuration and switching to a new configuration (none of which are source-controlled as part of FooBarix itself). This also provides the ability to downgrade the configuration, should it prove necessary to back out of 2.0 back to 1.3.