How to create a commenting system for ECK entities, similar to node comments as exposed field under the body?
As an alternative to the Comments Entity module, and the bug you reported about it, you may want to give the Reply module a try. Some more details about this module, from its project page:

Reply is a D7 answer to entity comments.
Reply is basically a fieldable entity so you can create a 'review', 'comment', 'forum post' or whatever you like by creating bundles and attaching fields to them. Such bundles can be attached to any fieldable entity by 'reply field'.
You can set access for reading and writing, position the form to the same page as entity or to a custom page, allow or deny replying to replies(= no hierarchy), choose threaded or flatted list. Such settings can be set for bundle, field, instance and entity with build-in inheritance which makes if a four level hierarchy settings system.
Most common usage of this module is comment replacement and reviews.

Even though this module only has an alfa release for D7 (as compared to a beta release for the Comments Entity module), the issue queue statistics seem to be more healthy:

Reply:  66 open, 166 total (about 40% open issues).
Comments Entity:  10 open, 10 total (= 100% open issues).