it's something to do with how their software treats the OSX executables.
The executables and binary data files and things like that are all fine. The only thing it seems to affect is shell scripts, which seem to be fairly uncommonly used by games these days. Actually, the only other time I remember running into one that was Steam-related was a temporary one for I think Trine that was posted to the forums that was to fix a bug before they could roll out a patch. Not really an excuse for them to have it broken, but might be why they're not in a hurry to do something about it.
They are pushing out updates from windows servers, which is where the line endings come from to my knowledge.
I suppose that could do it, although there's probably some way for them to work around it (which might break other stuff, or at least require a lot of testing to make sure it doesn't). Who even uses Windows servers in the first place, though? I suppose the original Valve team all came from MS, though, which might explain it...
Something you might be able to do if Valve can't/doesn't change anything, depending on how all that stuff is set up, is to replace the shell script with an AppleScript. It wouldn't surprise me if raw AppleScripts themselves have the same problem with line endings, considering they're probably not designed with "existing on anything other than an HFS+ filesystem" in mind. However, you can compile them in the script editor, which should get around that. You can also trivially convert the shell script to an AppleScript by using whatever the AppleScript command is that calls whatever string you pass it as a shell script.
Ok, just double checked, and it really is as simple as:
do shell script "<foo>"
You can stick that in the AppleScript Editor and compile it from there or just in a plain old text file and use the command line tools ("osascript" runs scripts, "osacompile" compiles them, man pages have the gory details) to do it that way, et voilà. I just tested a "hello world" script on my MacBook with HFS+, uploaded it to a Linux server (I think using ext4?), downloaded it on a Win7 box on the other side of the room using NTFS, and copied it back over the network to the original computer, and it still runs "echo 'hello world'" like it's supposed to.
Edit: I have no idea why this just occurred to me now, but I thought of a couple details that I meant to mention. The results I got do not guarantee that it would survive Steamification (I don't know the details of how it works, never having worked with them myself), but they're encouraging. They do mean that it doesn't use the resource fork of HFS+ in any way (yes, there are still
a handful of OS X features using it these days for some bizarre reason, like text clippings), which is good. The file transfers were also done with SFTP, HTTP, and SMB, for anyone playing along at home, and it seems fine as plain old binary data just the way it is.