Where should I store my build configuration files?
Normally the build configuration needs to stay consistent with the product code, so it should be stored into the same git repo as the product code.

It's true, the file would get merged when a branch merge from the parent is performed. 

But often it's a trivial (empty/fast forward) merge - if there were no changes to the msbuild xml file in the parent branch. 

And if the merge is not a trivial one it means there were changes in the build process in the parent, which need to be taken into account in the child branch as well since it also picks up the code updates that go with those build changes. In other words the msbuild xml merge is required in such case to avoid build breakages.