Fractal Terrains doesn't always produce good effects with its painting tools, though. The biggest problem (for me, anyhow) arises when using brushes in the polar regions. The brushes begin to squash oddly when displaying in any projection except the default equirectangular and they won't go over the pole. The brush engine is also fairly primitive and fairly slow.
Wilbur's brush engine has the same capabilities for brush wrap that FT's does (click the little "C" button on FT's Paintbrush Options toolbar and you'll see the same UI as in Wilbur), but it seems that I didn't expose wrapping on the UI. Some of Wilbur's filters (notably the precipiton) offer east/west and/or north/south wrapping options to allow for "spherical" or "toroidal" height fields.
There are some fancier tools like Mudbox or zBrush that should be able to do this sort of thing, but it's not really what they were intended for. If you're looking for something that lets you paint effectively zero relief onto a sphere, I'm not sure there's much out there because it's a fairly specific desire for a very limited audience.