Wow! I hope I didn't inspire you to go through that trouble
This tutorial won't hurt the upgradability of the setup. I installed netatalk on my server two or three years ago now and have upgrade through like four versions since then.
As for the custom version... good question. I followed this tutorial: http://www.kremalicious.com/2008/06/ubu ... ne-volume/
(also where I got the download from). I would have just simply recommended the site, but there are a few things I changed and made work a little better (the kremalicious site didn't leave me a working setup at the end of the tutorial). The stated reason why a custom .deb of netatalk is needed is because the Ubuntu repositories don't have the version built with SSL, though I have no idea if this is true. If these guides have you doing the setup without the custom version of netatalk, by all means, give it a spin and see if it works. Installing the version from the Ubuntu repository should also fix the dependency issue. Give it a try and let me know:
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sudo apt-get install netatalk
If you can get it working without the custom version of netatalk, I will remove that from the guide (and also change my server