In regards to your question though, both Logstash and Filebeat use doc. You are right about Elasticsearch being different though, I will raise that internally.
Whatever you choose though, it just needs to be the same if you have different sources going into the one index.
When using available elastic.co docs on migration from 5x to 6x people will end up with documents not being indexed.
According to the docs they will create _doc mappign type name so it will be good when 7.0 is released
Then they will remove document_type settings from logstash(cause it is deprecated).
They will end up with error the final mapping would have more than 1 type: [_doc, doc] because logstash will set doc and elasticsearch based on mapping will set _doc.
Or maybe I am doing something wrong - but thats what happened to me
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