Adding Html in text editor automagically adds undesirable paragraphs when publishing

While this sounds strange behavior, it does sound like you are doing it wrong. The wordpress “text” editor is not an HTML editor and should not be a replacement for one. It is useful for fixing whatever can not be done with the visual editor, but no more.

If you need a specific design which is just impossible to even get close to achieve with the visual editor, you should just create a page template for it. (It is unlikely that a author which do not understand HTML will be able to maintain the changes you are trying to do now, so no flexibility will be actually lost)