Using autotags for clickids is a bad idea as it was never its intended purpose.
The following links are to our existing wiki articles which are written from the admin perspective. We are creating a new affiliate oriented wiki article on tracking with passthroughs.
https://tmmwiki.com/index.php/NATS4_Additional_Tracking specifically "Subscription Passthrough Variables" are what you should be using to track clickids.
The current hold up you are referring to is that for a long time, the ability for affiliates to use them was off by default in NATS. On NATS versions 5.0.2.2 and later, this is now on by default for all affiliates. If there is a NATS install you are trying to work with that is having trouble, they can submit a ticket and we can quickly turn it on for all of their existing and new affiliates at their direction.
Once you are passing variables in with passthroughs, you will have access to them via affiliate postbacks
https://tmmwiki.com/index.php/NATS4_...e_Postback_New
Again, both of those articles are from the admin's perspective and we should have a more direct article from an affiliate perspective up soon.