The problem is that as of yet, the Live API (that lets project-gc and others access data from geocaching.com) does not grant access to bookmark lists that aren't public. As of yet, your ignore list on geocaching.com is private and there is currently no way of changing that - either for you or for the makers of project-gc.com.
You could, as you suggest, redo the list as a public bookmark list on geocaching.com. Then you would potentially run into the same problems as this guy:
The other option is for project-gc to implement a feature that would allow their users to maintain their own separate ignore list that they would then have to maintain separately from their ignore list on geocaching.com.
The third option is to wait for geocaching.com to change their Live API (and for project-gc to then work in the changes). That would be the one I would prefer - but then again, my ignore list is small. I tend to go find the caches instead and then remove them through the "Remove my finds" filter ;)