It's just as Sol said. How you word your document and present it is simply a matter of personal taste.
Wrong, you word and present your document to communicate your vision and ideas in the best way possible to the intended audience. If you don't structure a doc in a way that is clear for others to follow AND to refer back to, then you will be the only person reading it. Your personal taste will shape your judgement of what structure is most effective, but it should never be the sole reason for your choices.
Game Mechanics are, in essence, the set of actions available in a game, and the rules and limitations that govern them. I would stay away from anything like precise numbers, but I would include a description of the intended effect of the rules. Don't say how many rounds a pistol has, but what kind of behaviour and damage you expect it to do, and when/why you think the player should use it.
Definitely stay away from level and mission design (other than as examples) when describing game mechanics.
Game Flow would normally be a description of how the player's actions and objectives follow one another at the mid and high level. For example, the high-level game flow of a Total War game is radically different from the flow of a campaign game like Starcraft; the mid-level game flow of a GTA-style open world game is equally different from a linear shooter like Quake.