Thanks, Minetus

and thanks for the feedback.
Cutting out doors and windows I've thought it through and no it doesn't really become too much of an issue

You see, the Klyro's use special techniques to cut doors and windows out. The thing is, to heal the wounds you need a lot of what I would call "Calcium-paste" which the Klyros have developed themselves.
It goes like this:
First, the Klyros start cutting out the shell by delicately hammering small chisels(so that the shell won't break too much) to where the cutout should be.
Second, when they have enough chisels(which are maybe out of stone, btw. Flint would be a good choice) chiselled in the various areas they start pumping out the slime-like Baku creature(yep, have an unconditional love for slimes^^) in that area.
Third, now you need to be quick. When you've emptied the area all of slime-residue you smear(on the exposed areas, before the slow-floating goo gets out) this special paste which is a fast drying fluid in dry air, on exposed areas, before the slow-floating goo gets out. And now the cutout's done and you maybe either pump it back in or leave the energy-rich slime remains.
This goo is only a part of the creature(god, I don't want to explain how to creature looks

) most of the creature isn't vital, but an energy storage. The energy storage increasing is what makes it grow btw. It's like a blob.
Hope you understand, I'm happy you're interested.
Concerning the idea of floating 
I*m thinking air filled leaves, these could be made out of a local plant we could later make. what we do is tie 5-6 leaves in a ring with bound stalks so it floats on a ring of tied balloon leaves^^ Your idea sounds very interesting, though. You mean a floating pimp-stone? I could thinks of it being all hollow but that would make it too vulnerable and the shell will be weaker in the outskirts of the skeleton. Hmm, I don't know if it would be evolutionarily possible as it would have lost its limbs to some better method. Also, remember that they live on the seabed, sucking nutrition from the water and seabed. That Baku I told you about was just a stray so it wouldn't be natural to put pillows on a sealubber. Though, that's just my opinion, or else I could tinker a bit with the creature's lore and add a similarity to the portuguese seaman, a colony of jellyfish floating on the surface, hunting with its 10 metre long tentacles.
Edit: The above was an explanation to how you create doors and windows in the Baku, by nature it is completely hole-free and it's got nothing other then a couple of roots and a bubbly shell made out of calcium
SO you can make it into practically anything