If you still want to emulate the antics of SS13 in space, you can always build floating fortresses. Shutting off [CAVE-INS] generally will help out with this; or at least having some sort of anchor to retain cave-ins.
For other items of interest that can contribute to the mod, I think the Wasteland/Fallout mod should have some items here and there that you can apply/base off of; like the cement factory and arc reactors.
Always an interesting thing to implement, if possible, is to be able to collect blood, and produce clonexadone to produce synth-meat. Of course, synth-meat, due to how broken it could become, should have a risk of poisoning due to not being entirely natural; especially in raw form. However, if in an evil biome, I don't know if synth-meat should have a chance of "awakening" or not.
As to not render chemistry stations and the like from being horribly broken, what can help is collecting the necessary raw materials the ingredients would come from, and use material processors to break them down, and a centrifuge or something of the sort to finalize the processing of the material. Naturally, beakers, vials (and chem-safe barrels), and such will need to be be produced to contain them.
Using syndromes, all kinds of grenades can be used/produced with the various properties they can be given, when produced right. Even my personal favorite, Peyote-nades (space drugs in gas grenade form + whatever else I feel like including in them, like polytrinic acid, for example), can be produced and used.
Thanks to the customizability of DF and raws, I think we can make more varied chemistry reactions, and ways to make use of them. Explosive thermite boulders anyone?
EDIT:
For alternative building materials (and a way to spend some excess chemical resources), you can always combine a chem-station to produce sodium chloride, and use a synthesizer which takes that product, and use it to produce rock salt boulders/(blocks from mason workshops) as a cheap 'n' easy building/crafting material; alternative to green glass and cement.
If possible, within the limits of the technology of SS13, and some coding in DF, you can always build a well over a saltwater source, and have sodium-chloride as a byproduct of desalination plants (as a workshop; not the screw pump method). Produces clean drinkable water, and cheap building materials (along with chem-station ingredients; especially when separated through a centrifuge/chem-processor into Chlorine and Sodium separately for other uses in a chem-station.) when processed in a material synthesizer. Should make beach and island embarks a bit simpler to take on without needing to breach an aquifer.
Naturally, to make an effective desalination/water purification plant (to clean murky and blood/vomit/toxic water as well), I would advise you bring at least a block/bar of activated carbon or few to produce a proper desalination plant. Of course, to produce activated carbon, you'll need a forge of sorts to process raw carbon into activated carbon. Besides desalination/purification plants, activated carbon can also be used for cleaning materials, and air scrubbers to remove miasma for areas where they tend to come up often. Dwarves/crew members that stop around air scrubbers/purifiers get a happy thought from "tasting delicious freon" or "smelled clean air".
REFERENCES:
https://en.wikipedia.org/wiki/Activated_carbon (amazing stuff with plenty of SS13-DF potential; even compressed into building blocks (which material grinders can grind back into a powder (speed up transporting it from one part of the fort to another, sparing sand bags in the process); with other materials as well), would make an interesting looking building or craft/statue to show off.)