The design of Citadel Station makes sense when you look at it past the dated graphics and design; For instance, the strange maze-like areas you come across on the edges of the map are maintenance areas which tend to look more 'industrial' compared to the rest of the map, and are often in disrepair or are completely damaged due to Shodan remodeling the station (i.e, the resistance base on the medical level). The normal areas, on the other hand, are designed with standard textures and often have more 'civilian' style doors. Once someone makes this designation then a lot of the level design makes more sense.
The music that plays in the Reactor and Engineering levels is a music very similar to Nine Inch Nails "Head Like A Hole". Those two levels are set in industrial settings, and Nine Inch Nails is an industrial rock band.
SHODAN's electric stuttering may have an in-universe explanation; the corruption of her sound card may have been caused by malware that removed her moral inhibitors.
Re-enabling the Restoration Bays to their original function of reviving the player rather than cybernetic conversion is accomplished by flipping a large, conspicuous switch. Doing so causes a very computerized voice to loudly announce that the cyborg conversion process is disabled and that normal restoration procedures are online. This implies that cyborg conversion is an intended built-in feature of the restoration bays and that SHODAN just had one of her minions flip the switch.
Given some of the additional in-universe lore the remake adds, this quickly ranges into Fridge Horror territory if you notice that one of the citizen classes in Tri Optimum is "Mutant"...people who "have given their bodies to STEM" in order to pay off debts of over $50,000. There are tens of millions of people listed as being in this 'class'.
