Mytran wrote:

"Of course with my layout decribed above there is no need to give up these two engine rooms at all! 
The ease at which the S1 engine room set mirrors itself, allowing an 8' gap inbetween is a piece of design which impresses me as much today as when I first saw it - it really would be shame not to make use of it."
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Indeed, although the rectangular nature of the transporter room would make it an interesting alternate candidate for the starboard side but I presume the majority of fans expects a symmetrical arrangement here.
Mytran wrote:

"I would also like to use full-length "cathedral tubes" but unfortunately the directors of different episodes couldn't resist shooting the set from the wrong angles, so bang goes that forced perspective illusion!!!  "
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If you're taking it too literal, yes, but I feel very comfortable with the original producer's intention which was to show us a cathedral that extends further than what was actually there, though according to my estimates would still be limited to a depth of 8 meters, judging by the tube's diameters and the space in-between these (illustrated on my engineering deck 9 draft).
Bob