Humm... the effect does use the base 10 guideline (a highly unnatural liquid or gas) instead of base 3 (liquid or gas). Personally, I'm convinced.

A CrAu spell creates a wind, not literally air as we might think of it today. Is the air we breath that wind, or is it a side effect of that wind that is no longer magical by the time we breath it?
That's a very good question.
Suppose Dolabrius is in an old, musty, sealed room, with unbreathable air, and uses the power. Something happens, triggering a conc. roll, and he fails. The air immediately becomes unbreathable again? Or there is some time, because the air inside the room was purified?
My initial reading of the spell is that the air immediately becomes unbreathable. That the spell doesn't purify the air, the magical breeze itself is breathable, and thus needs to penetrate. Just like you can't drink magical water with an active parma.
But there's room for disagreement, and I'm not dead set on this interpretation.

The flying castle from Legends flies at "the running speed of a horse" (often also stipulated as 40mph) using the same guideline?
Yeah, and it's unreasonable. Can I use a base 3 ReTe to target part of a mountain and make the whole mountain move?
Later books are not always consistent in usage of rules. Some of the most problematic "canon" spells come from them (problematic in terms of "how does this even fit within the hermetic framework of magic").
Picking appart the effect in the stone disc from Legends of Hermes, it also lacks magnitudes for complex movement, "this spell not in effect" isn't an environmental trigger, an the disk, while controlled by light, lacks any kind of suitable trigger for that. Indeed, it's suggested a few times that the disk might not be an hermetic device, or must at least involve some kind of breakthrough.
Regarding the flying ships from TME, they explicitly add magnitudes for the extra speed (and for complexity of movement, for that matter).

The intent is kind of a rolling/flowing effect of the whole area of ground that the group is moving on, like a people mover/escalator kind of thing, for acceleration ... but putting it all back afterwards so that the spell doesn't tear up the countryside and leave a blatant trail to follow as well.
Some kind of large scale geokinetic surfing?
But I'm still having trouble visualizing how this can be done leaving no traces w/o a quite a few additional mags. And it doesn't really fit a combat engineer either, does it?

I think that depends on how one views the concept, though I think as we (Nithyn and I) discussed it the primary element of the concept in mind was that of the engineer.
When I said he is a combat engineer that happens to be a badger, don't take it as criticism. It was just me stating a perceived fact... that happens to be true, isn't it? The initial concept does seeps through the character.
I don't think it's strictly necessary to write a background for his transformation (and is Julius a transformed human or an oject who developed awareness? I think we can't tell for sure, but that's neither here nor there).
I still hold, nonetheless, that his powers are all over the place, both in required arts and types of effects. Again, fact, not criticism. To me it feels like he should be a magus (or at least was designed as one) instead of a magical creature, tbh.