1) The list of layers only shows the top layers, including duplicates and soil. Soil layers are usually 1 z-level thick, stone layers are about 5. If you see 6 stone layers listed, then you know what stones are in the top 30 or so z-levels. Most of my embarks have had about 150 z-levels to the magma sea, so there is plenty of room for other stones that are not listed. Marble could just be very deep.
2) Having flux makes creating your own steel much easier, but it isn't the only way to go. Depending on the civ, you could be able to order all 5 types of flux from the Dwarven caravan. If you max the trade request, you will get 4 of each type you ask for. Also, you can order pig iron and steel bars, or steel items to melt back into bars. Greaves would probably be the best for that, since trap components are extremely over-priced.
3) Flux for early trade goods was necessary in 40d, but with metal ore coming out your ears in 31.x you can do better. Tetrahedrite, galena, iron ore, native silver, and native gold are all more valuable than flux or obsidian, and a lot easier to get than in earlier versions. Also, green glass serrated discs are worth 252 dorfbucks before quality modifiers, and metal trap components are worth even more. A proficient Herbalist and a proficient Cook can turn out a lot of +prickle berry roasts+, and probably buy most of what you need from the first caravan.
Basically, flux is only really important if you want to make a lot of steel. There are other metals that will work for weapons and armor, other ways to get a little steel, and other trade goods you can use, even in an early fort.
JMZ