Neither volcanoes nor magma pools affect the contents of the geo biome (which is where inclusions are defined), and I believe the depth of the HFS follows by various world gen info, with volcanoes and magma pools being generated against that backdrop. However, the Volcanism value affects both geo biomes and where volcanoes (and probably magma pools) form.
I know there was a case in the past where spires reached into the sky, but I thought that was fixed. The current data structure as mapped by DFHack specifies which layer the spire reaches, with valid values being cavern 1 - magma sea, with a bug causing spires to go AWOL if the world has doesn't have the cavern the spire is generated to reach, so they won't appear for the most common cavern case of cavern 3 if there are only two layers (the logic ought to count caverns from the bottom for this case, but it doesn't).
Now, if you hack the mid level tile info to have the surface below the relevant cavern you ought to get a spire in the open (as well as probable cave-ins), but then you're heavily into hacking territory.
Embarks with large elevation differences tend to result in a longer distance down to the HFS in order to fit the caverns in. Also note that everything with an elevation of less than 100 will become ocean (again, you can hack the mid level tiles pre embark, but DF won't generate that naturally), and so not particularly suitable for embark purposes, and caverns ought to be generate below the ocean floor anyway.