What are the stability differences between, having the bubble/sphere the top vs bottom?
Generally you want underwater vehicles to be statically stable. This can be most simply achieved by keeping the center of buoyancy above the center of mass. The exact degree of stability is more dependent on relative moments of mass and buoyancy, for lack of the more technical term.
In short Bubble on top of the ROV relatively good stability, perhaps an improvement in stability, maybe not, if it shifts the relative moment too much. Bubble on bottom of ROV is going to negatively impact static stability.