As far as i know it from other Engines, Spine exports a signle File (XML or something similiar), which you import into Visionaire. I don't think you have to re-import or rebuild the bodyparts.
About the Pixel art, i think that's purely a matter of setting your scaling to nearest neighbour. In my opinion, Cut-out-style animated Pixel-Art seldomly looks good, because of the low resolution that makes rotation of joints look "wobbly". Take a look at a Game called "Distraint" on Youtube. It's Pixelart but animated with after Effects and even though it's a great game you can see the effect quite clearly.So it's not so much a problem of Visionaire than just of pixel art in general, that deformations will never really look that great especially when compared with frame-by-frame.
Personally, i've never worked with Spine before but i did quite some cut-out animation with Toon Boom Harmony, when i was still wanting to make my game in higher res.
http://joelmayerprods.tumblr.com/post/130347568768/next-up-w...I kinda like working with Vectors better when it comes to deformation, because it's more forgiving. You can do things like breathing very easily and i didn't even had to separate each joint:
http://joelmayerprods.tumblr.com/post/119051773064/idle-anim...Second Walk Cycle test for my larger Game:
https://pbs.twimg.com/tweet_video/CFebNdwXIAA2eif.mp4Toon Boom is able to export XML Files as well and is very well integrated into Unity. I sometimes wish it was more widely accepted by other Engine Developers as well, because for me it's the best Animation Software out there.
Of course it also exports any image Sequence you like so it's still a valid option.
But since i got away from doing really Hi-Res Art, i'm pretty Happy with Aseprite