You're right, totally exposed lava lamps in a carpeted lounge make for a far more realistic portrayel of a matter/antimatter reactor and it's engineering assembly.
At least it represents a bit more of the clean-room aspect you would expect in such an environment. And you can actually justify having the transparent rig so as to provide visual inspection of the flow. It'd be like having all the medtools of the time, but the doc still taking your pulse by hand, because he can gauge by his natural senses as well as via tools.
Don't see how you can justify the 20th century pipe fittings in any 23rd century context, or why you would want to.
That's my line of thought. That and brewgineering just is stylistically out of sync with the rest of the look of the ship's interior. And it's not the dirt and grim, it just the jump for future tech to modern industrial. You could take the TOS style engine room, redesign it to work with the other interiors style and still have brewgineering underneath all that as being the guts that aren't normally seen.