This setting may seem small and annoying, but for new users, it's a big deal.
The setting controls the presence of a hyperlink to the documentation allowing people to troubleshoot problems with projects that NCrunch has never been able to build before. If this is moved into the .user file, people will get notified of this for projects that are already configured by other team mates and have been built by NCrunch correctly.
How is the flag causing problems for you? Does it trigger your VCS to think the file has changed, when it actually hasn't?
If you're concerned about the config files polluting your VCS, you might want to look into this setting -
http://www.ncrunch.net/documentation/reference_solution-configuration_project-config-file-storage-path.