Breaking out the bottom of the plant is a good idea actually... I've heard of betta's getting curious and getting stuck in the hole at the bottom. (I could imagine Aegir doing that... lol) Just sand down the edges, and it will be fine
My thoughts about the paint... maybe you could paint it, let it dry, and then apply a thing coat of aquarium safe silicone on it to seal it?
I grew up with reef tanks, and when I was in elementary school, I would make all kinds of "decorations" for our tanks. My mom would coat them in the silicone, and we never had any issues.
And some of the corals and fish we had were really delicate.