first of all thank you for the couple of beers you offered, I'll probably have them tonight eheh. Back to the issue, the theme author is indeed right, I was using the filter hook suggested by WordPress' core developers in my plugin, or at least the one used in their default theme. Now that I changed it to "post_link" as per their message, get_permalink() works as expected. Thank you for your feedback on this. I'll release a new version that includes this fix soon.
As for the "native" management page, this was how my plugin worked at first, but then people started to complain because they didn't want this page to show up in their navigation
I was a little skeptical at first, but then I agreed to change the way my plugin works, generating this page on-the-fly. See, this is the problem: WordPress has a big community around it, and of course there will always be users who want A and others who want the opposite of A. It's impossible to make everybody happy, but so far the approach I've followed seems to be the most convenient for the majority of my plugin's users.
I know this means having problems in cases like yours, but I'm more than happy, as you saw, to offer my help to solve them. Also, this workaround of creating a page and assigning it to Subscribe to Comments, should help in most of the situations out there.
Long story short, please let me know if you have any questions about the page you created and how to load widgets in that case.
Have a nice weekend