You could of course export/import those settings.
The other approach is to enable project specific settings for some settings.
We have a very small Git repository with those kind of files:
.settings/org.eclipse.jdt.core.prefs(compiler problem settings and formatter rules)
.settings/org.eclipse.jdt.ui.pref(cleanup rules, common code templates)
The common settings are just copied/merged in each projects
.settings directory, ensuring common rules amongst all projects, whatever the workspace.