Every time this comes up, it sounds like a straw man. Okay, an accidental straw man, but still.
When do we see ships oriented in a "common plane"? Only when they are within visual range of each other, and deliberately maneuvering in acknowledgement of the other side. Why would they not orient themselves according to some spatial rules of courtesy when they meet?
They could fly whichever way when they are distant from each other. But when contact between friendlies is made, it would be customary to roll the ships to the same orientation out of sheer politeness (indeed, we see the Reliant do a little courtesy roll when she first meets the Enterprise - although the maneuver actually makes her look a bit menacing).
Also, when numerous friendlies operate together, they no doubt assume a formation of some sort. We have seen formations of dozens of ships, and later hundreds or thousands. In formations that large, it wouldn't make much sense to have a complex geometry; better just to place every ship the same way up and the nose pointing in the same direction, so that commands like "Everybody hard to starboard!" are unambiguous at the initial stages of the battle.
When the battle degrades into a furball, ships on one side may try to maintain an (arbitrary) joint "down" to retain some semblance of situational awareness, even when they roll and climb and dive a lot. And the enemy might be obliged to do likewise in order to conduct the battle efficiently.
Similarly, when two opposing ships meet, they might choose matching orientations either out of (false?) courtesy, or then simply to bring their weapons to bear in an optimal manner. Shipbuilders would realize that the most likely starting point for a battle is with the ships trundling towards each other nose first, and would install the main guns and armor accordingly; captains would then deliberately seek nose-first confrontations, and would thus already be making "arbitrary" choices of geometry.
Ultimately, such diverse rationales would reinforce each other, until it was general naval tradition to orient ships the same way - even when it makes no immediate practical sense, it's something that everybody can afford to do.
And ultimately, it doesn't need to make any practical sense even in closer analysis. It would be a bit like saluting shots. It is counterintuitive that firing a bunch of guns would be a sign of peaceful intent. But it has become fairly universal, remaining in use even when ships no longer depend on slowly reloadable cannon that become unthreatening after firing a saluting shot - indeed, even when ships no longer carry any cannon except the saluting one.
Timo Saloniemi