you can turn off all the caverns, underworld, and magma level. then at the lowest map points you will still end up with ~50 levels below ground level. I tried it before. magma level is on if underworld is on. underworld can be off without turning off magma level. I think that the ground level has something to do with depth of oceans/water features as the lowest number of layers I had was a non ocean map with a lake/sea centrally located and I was just off the shore line, bet if I had checked the deepest water level was 50 below.
If you really don't want deep water formations, then you can set the lowest map height to 99 (0-100 = oceans/seas). the highest map height needs to be 400 for dwarfs to make a start home on the map. haven't tested it for nondwarf player races, I was still playing vanilla DF when I was really testing out the map preferences.
for height above ground you can either add them in manually with DFHACK, I think its infinitesky or something like that. or you can edit it in the preferences, there's an option for layers above ground, think 15 is the norm. basically it just means the highest map level is the top ground level+15 wherever you embark at. personally I would use infinitesky as you can add layers as needed and there was an auto option for it that would add a layer as you built upward (if I remember right if you built anything on the top layer it would add just 1 layer, but it might have more options now.)
The only thing I see that would be serious problem... you wouldn't have access to any underground plants, along with demons, most major boss type creatures... but if you're just wanting to build (say a human race because they can't stand being underground for very long) then that shouldn't be a problem.
EDIT: So I went and messed with the settings with 90 as my lowest surface level, 400 max, no sea border, 1 cavern layer(apparently even humans need 1 or it crashes saying they can't find any vegetation for farming!?! lol) and a magma level, no underworld... I have an embark site with only 17 Zs below ground. Perfect for a human civ. But should be capable for any race.
The dfhack script is infiniteSky. start it with "load infiniteSky" (S must be capital). Then enter "infiniteSky enable" to start watching for your constructions above that level. the only bad thing I couldn't completely remove underground caverns... If you remove the magma level, you could probably get down into the 10-15 Zs but you wouldn't have access to magma furnaces/forges, without using magmawells(dwarves/succubus) or fluid casters(orc), or dfhack (liquids/feature). But I'm not sure if you want magmashops.