I'm also curious to know what led you to try that in the first place . . . But practically speaking, it doesn't seem like something that arose out of necessity, or maybe I'm just not seeing it.
The short answer is that a fully manual flight mode won't give me the results I'm looking for without a flight model that is both less forgiving, and requires much more complex and precise input devices such as a full on HOTAS. Even in Tiny Combat, which does have a fully manual control setup, you can't get the level of precision, smoothness, and the "cinematic look" I'm after without fancy hardware. There's a reason I call out Star Citizen in the the game's page, and it's because that kind of flight model and control setup just doesn't lend itself to good landings.
This goes back to the helicopter stuff I was talking about. Helicopters fly like both helicopters and planes in a realistic sim (i.e. DCS) and it's all controllable because you aren't flying this on a gamepad, and you are doing things at a much slower, more controlled pace. You can't whip these things around like a video game sci-fi spaceship, the way I'd like to be able to, because the physics just doesn't work that way. So to give that faster pace, and more responsive handling, you need to up the power on everything, exaggerate the physics, and so on. However in doing that, it also becomes even harder to control. With a mode switch, you can adapt the controls, filter them, tune them, to specific regimes of flight and make it very controllable. It's similar to how aim down sights completely changed how FPS games were made on console. When a player uses ADS, they are expressing their intent to precisely aim, and you can lower the sensitivity, snap the crosshair, and change how recoil is handled.
Without some kind of mode switch, the only other option to make these kinds of physics controllable (and good looking enough, which is the whole point here, this is a very aesthetics driven project) is for the ship to massively change in behavior on its own. The way that the throttle blends from lift to main engine in the "manual" mode is actually vestigial from experiments on that, though I liked it enough to keep it. Not all ships behave this way either, e.g. the aerodyne that's not in the prototype doesn't use the lift engines at all in the manual mode. So there will variety in how things fly and control. It's also an avenue for me to experiment in different control methods and physics. However the problem with some kind of magic blending that somehow deduces what the player is trying to do, is that inevitably you're going to guess incorrectly about what the user wants to do and that feels really bad!
The modes communicate the player's intent, and from there you can optimize the two modes for their own special purposes. If you want to hover in a precise and tight controlled area: hover mode. If you want to land vertically: hover mode. If you want to fly somewhere far away: normal mode. If the player doesn't understand this, and is trying to use the modes for things they aren't designed for, that is as I've been going on about, a training issue. A good tutorial should cover this, but at the same time I don't think it's a problem that the player might have to learn and practice a skill. That's kind of the whole point here.