If a conjuration can be moved horizontally over a pit and follow (mildly-sloping) terrain up or down, then, for consistency, it can effective fly or descend at will - your will. After all, a pit is nothing special; it's just a region of lower altitude. Apparently you can either follow the terrain down or float over it.
It's not necessary to permit it to rise in altitude without terrain to support it, though that's be a slightly weird distinction.
In any case, the rules don't have much of anything to say about 3D in general, so I'd try to just let it fly... ...and deal with balance problems as they arise. Not permitting arbitrary 3D movement forces the DM to choose for each and every conjuration a bunch of limiting factors without any guidelines from RAW, which doesn't sound ideal to me.
It's not like conjurations in general nor the spirit companion in particular actually do particularly much (such as carry things or manipulate doors or whatever), if I'm not mistaken, so I hope this isn't a balance problem.