Mmm, the problem with a fleet-wide withdrawal is that the entire stated purpose of this feature is to preserve individual ships as well. Repairs take less time than construction, so a key part of the present situation of decisive battle is the annihilation of the enemy fleet which forces them to rebuild losses from the keel up. If you simply pool fleet-wide HP and retreat when it drops below half, that damage tends to be focused on a few ships. The retreat thus means that half the fleet escapes unscathed and half the fleet is annihilated, which doesn't fulfill the design goal; moreover, it can already be done manually in any battle that takes around a month as in the late game. By forcing individual ships to flee, you leave more individual ships intact and spread that 50% damage across more of the fleet. This preserves individual ships as well as the fleet as a whole and maintains the fleet as a force in being, making snowballing off of an early victory a bit more difficult unless you can catch the enemy fleet again in the repair docks.
Plus, I'm not so sure that the ships still appear when they've disengaged. That single lone screenshot we have shows two ships which I assume (without any proof, but I think it's reasonable) are the two ships listed in the status screen, but one of them seems to be flaring up. Depending on *when* they took that screenshot, it might be that disengagement is communicating visually at on the map by ships jumping out using the same method as Emergency FTL, and they simply took the screenshot at the moment this was happening because it was visually distinctive rather than simply taking a shot of one lone ship. Plus, both of the ships are still taking fire when we know from the DD that disengaged ships aren't targeted for fire in the first place, which suggests someone either screwed up big writing the DD (known to occur before) or they intentionally timed that screenshot pretty much right when the ship flipped to "engaged" to "disengaged".