I'm so glad you enjoyed and got to the ending!
About the stuff you point out:
- I've notice that once during all the playtest o-o I could not replicate it, so I don't really know. I'll check what you said.
- I think you were really lucky! There's a chance that every time a machine breaks one of the two (If able) will spawn. But there is a small chance of neither appearing! I think that's what happened.
- The upgrades reduce the amount of "punishment" for keeping a machine in a broken state. They reduce the rate at wich the clock advances towards the bad ending.
- And yeah, it's flavor text and lore. In Shaft-10 (The free game I launched with DtS) there are some more lore pieces and even some references to the eyes, for example. But yeah, mainly flavor text in there. In upcoming games within this lore might not be tho... :)