I would think separating them out would be a good idea - you know how long it would take AE to save a 172mb file each time you'd want to save. Even in the age of SSDs, that just sounds like a swampy, interactivity killing mess. At least with split projects you wouldn't get bogged down constantly by the sheer amount of keyframes you're saving.
But bigger picture - if it's a spherical rig, aren't you going to want to stitch it together first and then stabilize once? Seems like 14 different stabilizes would scramble my brain when viewing.