Floor transmutation into soil does not allow surface tree growth, because the rock beneath remains rock, so there's still no room for roots.
Caving in soil might works, although transmutation may cause it to fail. Trying to cave-in soil down into the aquifer caused the soil to transmute into the type of soil of the aquifer layer, but it did not take up the aquifer property.
Caving in a piece of aquifer soil down to the circus failed to retain the aquifer property, and I believe (hazy memory) it transmuted into rock as well.
I don't know if caving in several Z levels of soil has been tested to see if only some of them are transmuted.
I believe there is a DFHack tools that allows you to transmute tiles. If so, you could cave-in soil and then correct any transmutation by reverting the soil back.
Rather than casting obsidian on top of the caved-in soil, only to shave it away, I'd rather build a floor at a suitable level above the soil and cast obsidian on top of that.
Yes, digging out cast obsidian above ground leaves soil floors. If you do that on the surface level (I've done it on top of my surface level courtyard roof), sparse shrubs can grow on it, but not saplings. Tiles in the air have a no-growth flag set, I believe which disallows the natural growth of anything but grass (farm plots can still support crops, provided the air biome [= biome of the world tile to the NW, unless the particular air block has a biome shear in it {which is a bug}] allows it). You can recover some of the aesthetics by making a floor of obsidian blocks (but those can't be engraved).
Edit: I tried caving in a soil plug one step down into rock. This retained the lowest soil (fire clay) as it landed onto rock, while the soil layers above transmuted to match the soil layer present on that level. Caving it in one level further (5 levels further down), caused two levels of fire clay to protrude into rock, again with the soil layers further up transmuting to match the soil type of their respective levels.
Edit 2: I removed another layer at the bottom and replace the layer above that with built walls. As expected, the built walls were completely smashed away when dropped, and I now have 4 layers of fire clay down in the rock. I'm not completely sure, but the top of those ought to have been ordinary clay, as I dropped everything two levels, so the top levels of the dropped stack should have been clay with fire clay underneath, so it's possible just the act of passing the last soil level transmuted the soil to the last type.
Edit 3: Yes, I caved in all 4 soil levels a bit down into the rock in one go, and all 4 of them ended up as fire clay, so I assume they transmute to the last soil type reached on the way downwards.