It is possible using .gitattributes to specify the endings to use for different file types, however this seems a bit temperamental when checking out different branches with different endings.

To be safe I think we should just ensure all scripts copied to the AS distribution have the correct ending for their target platform.

Scripts used within the build are not as much as a risk as they are going to be checked out on the target platform that is defaults are used are more likely to default to the local platform.