Mordenkainen, in his second treatise on inter-dimensional dimensions, postulated that....
No, wait, that's not right, because....
The rules don't say
The rules don't define inter-dimensional dimensions. The rules don't define what an extradimensional space is, or a planar gate, or any of those related phenomena, in any detail. They're defined generically, if at all, and then the features that use them define how they work.
But to answer your question
"How can both (A) and (B) be true at the same time?"
Of course extra-dimensional spaces are going to mess with your dimensions. That's why they're "extra" dimensional. And how can "another plane of existence" possibly obey three-dimensional geometry?
2. You're mixing specific and generic
A Portable Hole is relatively well defined, in that we have a definition of a specific object.
The terms "gate" and "portal" are extremely generic, within the rules. If you were talking about a specific spell or magic item, then maybe there would be some answers.
It's perfectly reasonable that one gate or portal would allow you to throw a rock through to the other plane or whatever, but another gate or portal wouldn't.
Planar portals are discussed in the DMG in Planar Travel, under Planar Portals:
“Portal” is a general term for a stationary interplanar connection that links a specific location on one plane to a specific location on another. Some portals function like doorways, appearing as a clear window or a fog-shrouded passage, and interplanar travel is as simple as stepping through the doorway. Other portals are locations — circles of standing stones, soaring towers, sailing ships, or even whole towns — that exist in multiple planes at once or flicker from one plane to another. Some are vortices, joining an Elemental Plane with a very similar location on the Material Plane, such as the heart of a volcano (leading to the Plane of Fire) or the depths of the ocean (to the Plane of Water).
Clearly just from that paragraph, it isn't so much that there are different kinds of portals that can be cataloged, and you just need to find or deduce the list, it's that the rules provide a very general idea of connecting planes and allow for extremely diverse ways of connecting them.
3. The rules aren't built that way
The rules just aren't built ground up to be a perfectly cohesive unified whole that always makes sense. I mean, obviously, right? It's amazing they're as cohesive as they are.
As a Player
You're not going to find the unifying principle that allows you to exploit all of these things, because there isn't one. You can probably find individual cases, like the Portable Hole, that are mildly exploitable.
My best advice is to focus on specific cases that you think you're interested in exploring in your game, do your research, and discuss them with your DM.