I personally tend to favor some degree of consistency, and prefer dungeons with the basic amenities(food, water, shelter, safe passage, garbage disposal and drainage) in there SOMEWHERE. Beyond basic needs though, free rein goes, people make illogical architecture all the time anyway.
If the goblins did not need to have man high tunnels, it may be that they dug into a natural formation, or got the place second hand. The pit trap might just be a skillfully patched sinkhole, except it wasn't built to handle the weight of five humans in full kit, etc. Rooms may be abandoned from population pressure, politics or simply because theres a bad smell you only notice after you sleep in it.
What the basic amenities are great for is establishing structure and dealing with the unexpected. What are they doing if the PCs sneak in and avoid alerting the whole place to combat readiness? Ways to poison the lot of them, investigate their livestock and rubbish. Its the small trivial things you expect that are jarring when not found.