That's how it looks in the schematics, and the physical models I've seen, and all the other game renditions out there. It may not be 'right', but that's an issue to be taken up with the original design. I don't like the idea of running the pylons up into the bottom of the engine glow either, but, that's the way the ship was drawn.
I don't agree on the bottom of the ship not being worth the effort - SFC has multiple view angles, as do other games - not to mention the model programs. I give the same attention to the lower side of the ship that I do to the rest, otherwise the ship would simply come off looking halfassed. However, when there isn't much of a ship to work with in the first place, it kinda leaves me at a disadvantage. The Akyazi is a flat bottomed vessel that doesn't have much in the way of detail or physical depth. One can only do so much with a pancake.
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I don't have much use for pirate ships and I doubt anyone else does either. I already had my fill of trying to update low texture, low detail stock models with newer renditions (the KA Klingons and SFC Andros). Trying to work with the stock pirate models isn't really worth the effort since most people just use them for target practice...and the designs aren't all that appealing.
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As for the Akyazi viewports, that's the way the ship was drawn. Besides, windows are overrated...