Because of the general access problem with fileadmin/, i manage all my templates in typo3conf/. There i create a directory "templates" for example and manage my templates there.
In TYPO3 < 6.0 you have to set $TYPO3_CONF_VARS['FE']['addAllowedPaths'] = 'typo3conf/templates/';
to properly use your templates.
This also has the advantage that you basically only have to manage typo3conf/ in Git :)