Big discussions about tiny flowers… is this what gaming has come to?! 
Jokes aside, I haven’t tried the unstable alpha so thanks for the images. 
To add my opinion to the discussion, I’m not totally against the “floating” (when it’s because of bad resolution) but I get that people have a problem with it in this case. I think most of the problem lies with the green square however and that there is not even a hint of connection between that and the flowers.
I would suggest making it just a little bit more organic, removing a voxel to make a dent in the side and letting a dark green voxel dent the side of the light green square (not necessarily in the same place) or something like that.
More importantly I would add the lower halves of the stems, to show that there is a connection, even if you can’t see all of it.
About the glow, I love the thought of glowing flowers and have been looking forward to seeing it in the game. However, I don’t know if it’s technically possible yet but if you can then I think you should turn the glow off in daylight. Bioluminescence should not be strong enough to be noticeable in daylight. At least not if you go by the standard in movies and games. Take Avatar as an example. “Normal” jungle at day. Total rave at night.
You could even add to the contrast by making it rather dull during the day. Either by having a dark color on the flower or by letting the flower close completely, making the “flower cube” smaller and green.
Leaving the looks, I think it would make a cute scene if the flower could only be harvested at night so your hearthlings had to stay up late, walk around with lanterns, wade though fields of glowing flowers and get a late breakfast the next day.