Concrete under the tub?
Built in the early '60's, so here are my best guesses about what you describe:
1. A fiberglas tub and surround would normally be attached directly to the studs. Greenboard would only be necessary for a tile surround, if that's what you're going to replace the fiberglas surround or entire wall with.
2. You don't say what size pipe that is, but if it's not the main 3" or 4" drain/waste/vent stack and only 1.5-2", it is the vent for the lower level tub drain and right where it should be. All toilets drain into the main stack or main drain line, and everything else is, too, although with smaller lines.
3. The supply lines usually would be run the most economical and direct route from the main cold and hot sources. Directly down from the level above must be it, in this case.
4. If that's what it is, you might want to consider re-wiring that while you have the wall open. No junction box should be enclosed inside a wall, however. Have a solid length of new wiring run from the panel to the stove.
5. They probably left it like that in order to plumb the drain in the gravel to the specific tub or shower that was to be selected later. The fiberglas tub bottom should have been supported by mortar or compacted gravel under it, but if it ever leaked, they would never know it. May have been why they did it.
In any case, you can change the clawfoot plumbing as necessary much easier with the gravel, than having to bust out concrete.
After you've done the plumbing for the new clawfoot, making any adjustments and changes as necessary, then you can remove gravel and backfill it with 4" concrete level with the rest of the slab. If you're going to replace the tile, there should be no problem.
I assume that you're doing this work with the proper local Building Inspection Department permits and inspections. (Everything must be to local code.) If you're not, please stop what you're doing and get them involved immediately. If you ever want to sell that home, you will need the proper records, or you may be forced to tear everything out and re-do it later.
With what you've described, I think that this all makes your remodeling job a little easier, if nothing else.