According to this source, the original script describes the shaft several times as a factory:
INT. SKYPLEX - CORRIDORS
... The corridor has large windows along the side that look out onto the factory.
INT. SKYPLEX - FACTORY SHAFT
Mal lands on the torturer, slamming into a steel balcony that overlooks the abyss of the factory shaft.
INT. NISKA'S OFFICE
Zoe, Jayne and Wash come in. They rush to the open window, see Mal fighting the torturer on the edge of the factory shaft precipice.
Quite what's being built there, or why it needs to be built in a huge bottomless pit perfect for tossing bodies down, the script doesn't say.
Before looking to see if there was a script available, my initial thought was that the shaft reminded me of this somewhat similar-looking tech shaft from Serenity:
Although a lot more elaborate (which is what happens when you move from series to film...) it has a similar structure of large spinning metal elements stretching down into infinity.
This machinery was explicitly identified by Mr. Universe as his complex's generator:
They destroyed my equipment, but I have a backup unit. Bottom of the complex, right over the generator. Hard to get to. I know they missed it.