With a quick test I can't reproduce this with %40 as encoding, but I
will try some more later.

I would highly recommend to NOT write your authentication information in
sources.list through. Beside the parsing problem you seem to encounter,
you can't reasonably change the permission of the file (it has to be
world-readable to have apt-based tools in a functional state).

Instead, create the file /etc/apt/auth.conf and and use the netrc(5)
format to specify the authentication tokens. You can change the access
permissions to this file to your liking (600 for example) as a bonus.

Example: echo 'machine example.org\nlogin star\npassword hunter2' >
/etc/apt/auth.conf

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https://bugs.launchpad.net/bugs/1558484

Title:
  Ubuntu 12.04: apt-get can't parse repository url if username contains
  @ ('at' sign)

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