The Miranda-class's circular saucer semingly fits in Defiant's dock (or one of the three, anyway) as seen when USS Trial docks in "The Way of the Warrior", so surely an Intrepid-class saucer will fit pointing in? Well, depending on if DS9 is having a BIG day or not
In all fairness, the angle doesn't show like, the saucer actually inside. It might just be "bumping" it so to speak, and a gangway extends out.
Does the habitat ring actually have docking ports? I know they have runabout pads, but docking ports inside a larger ring specifically made for docking doesn’t really make a lot of sense.
I don't think the habitat ring has any docking ports; I don't recall any mention or reference to them. That said, I assume that all the docking ports we do see have extensible tunnels, even though those aren't mentioned, to accommodate various ships. Speaking of squinting and pretending, I tend to do that with the Yeager's secondary hull. Having put together both model kits that they built it out of, I get why they did what they did. It just makes no sense in-universe. Even if the Klingons build birds-of-prey to different scales, it just doesn't make any sense to me.
I agree, if we ever saw it close up the overall shape is there, but all the details are different. Sort of like how both the 33 incher and the 11 footer are both the TOS Enterprise, even though the saucers are different shapes.