The point for svn:eol-style native is to allow people to check out files and edit them on their own box and not have to worry about the end of lines.

If we set the style to LF, then people that do check the files out on Windows to edit will have only LFs and not CRLFs in the file and then notepad or other simple editors will get a file that appears to be one long line instead of a normal looking like file.  So svn:eol-style LF prevents people with Windows clients from editing our files easily.

Since we're only running the scripts on Unix OSes, or even Cygwin, then when we do a checkout there, the end-of-line is LF, so everything works fine.  Now, if we do checkouts on non-Unix OSes where the eol is not LF and need to run them and the script process needs LF end of lines, then there's an issue, but I don't see this as being a problem since we're very unlikely to run into it.  Even in Cygwin, most people have it run in LF mode, not CRLF mode.

I think you're trading a known issue that we can run into now (people editing these files on Windows systems and wanting to provide the correct system end-of-lines to make life easy) vs a problem which isn't occurring (running a script with CRLF on a scripting engine that needs LFs).