I'm giving my opinion here as a moderator of the cryptography site where this question was posted. This is to show that we take these kind of posts seriously, but also to indicate that this question is not particularly relevant to the site.

There seems to be a common trend among forums involving the topic of cryptography to shutdown any conversation very quickly, least in my experience.

First of all, Cryptography on StackExchange is not a forum. It is, like most if not all of the other StackExchange sites, a Q&A site. It has a community, but that community should strife for answering concise questions in the best way possible. In a very big sense, it is designed to avoid conversation as that conversation ends up muddling the result for future readers.

From the stand point of a newcomer to the field making bold claims and selling snake oil I can understand the trepidation and warnings.

A newcomer is not defined that way. A newcomer can make basic very basic errors. Of course, the annoyance will be higher if they are making bold claims or sell snake oil, and the response will probably be as loud or bold. But take the student of cryptography that submitted their cipher to the AES competition. That was received relatively well, even if it was broken almost instantly.

But as someone who has been reading the books, studying the courses, and experimenting with code when do they graduate to being able to ask educated questions and get more discourse beyond “thou shall not write your own stuff?”

If a concise and clear question then this should, at most, be a warning in a comment or a back section of an answer. If the question is good then it should be answered. It doesn't matter if the question is simple or outside of what is common. I'm most drawn into discussion here what makes a question good, but for that please read the help section of our Q/A site.

If you find that the question gets closed because "thou shall not write your own stuff" then please flag for moderator attention. This cryptography site is specifically for asking questions that are of academic interest.

Usually though, such a comment would be as a generic warning to the asker and future readers. I hope you agree that starting cryptographers should receive such a warning in advance. That should however in no way stop the question from receiving answers.

For example. I know enough to not write my own cipher. I use battle tested technology like AES-GCM. But what if my experiment wishes to use it in a different way. Maybe a communication protocol for a learning exercise? Or chunking algorithm that uses the cipher for larger payloads?

One thing that this site is not designed for is prolonged discussions about a elaborate scheme for a specific purpose. Doing a full analysis of such a scheme is pretty tough work. It will precisely lead into discussions, adjustments. It is also hard to conclusively answer. Somebody indicates a possible snag, a discussion will start, possibly a new trick is used to overcome the snag, but that doesn't say that the scheme is now secure.

At this point it is important that the Q/A site is designed to deliver answers to anybody searching within the site. This question now took up a lot of time, but it won't ever show up in search results. It is only of value to the person asking the question and maybe a person of two that was following the discourse.

Now you can still come back and ask "so what"? But as a moderator I would then indicate that StackExchange does have a set of rules and as a site we are incensed to operate within the rules. We can, and do challenge the rules sometimes, like we do with homework questions where we accept more than on other sites. However, in my opinion it would be very detrimental to the site if we become "a forum" where anything goes. In that sense SE works differently from newsgroups, reddit and Quora, and I don't think this will change even if site visits are dwindling.

Then again, if you would have this protocol and then ask concise questions about specific parts of it then this is fine. Generally, if your question post contains a single question + maybe one or more related questions then it is fine. If the question count goes to 4 then the question will probably get closed and five is right out. A lot of StackExchange is also about how to ask questions.

When addressing these application level ideas I find it very hard to get any dialogue or information because I’m not allowed to do it myself even if the system I’m targeting lacks something.

If you want to invent something, especially something that goes against established ideas then you need to be very stubborn. It's a trait that you'll find in any field. You do you. Just don't expect this site to accommodate you if you post something against the rules. Of course, being stubborn won't guarantee success - or a secure scheme for that matter - but not having it does probably mean failure.

My deepest apologies if this is off topic to this SE. I’m just at a loss on how to find educational discourse about cryptography and its use without the gate keeping that happens in this community.

As an elected moderator and gate keeper: if you want to do that then do it outside this community. If you want to have a chat or discussion about anything we have the Side Channel, our chat. If you want to make changes within the StackExchange rules then you can create concise, specific proposals here in Cryptography Meta. If you want to change how StackExchange works then there is StackExchange Meta.