Although I do agree, I do understand why it is done this way.
I made a post about it before here - Rich Text Editor Press "Enter" get two carriage returns - #3 by Daeraxa - explaining what I believe to be the rationale behind it but I do also agree that it isn't the 'normal' behaviour one would expect when migrating from a non-markdown system.
I agree it would be nice to have the option and I think there are quite a few people who share this sentiment so if somebody could make a proper justification for it and create PR for then there is a chance it could be considered.
It sounds like it is simply this option within TinyMCE config TinyMCE | forced_root_block
tinyMCE.init({
...
forced_root_blocks: false
});