Airtight Conveyors and/or Customizable Junctions.
Firstly, and the most modeling;
Conveyors need an armored variant so airtightness is not a drawback on the game's processes.
Let alone having a line of conveyors along the outside of your ship not looking pretty; simply covering them with the new armor plates isn't my cup of tea either...
Some armored conveyor lines would help keep the flush look and sim speed out of the negatives with the need for junctions.
The other idea, without much modeling;
Possibly have the junctions customizable when inside the terminal, you can turn on or off sections to negate the need for there always being a check of where items are going and can go every tick. Making it act like a... Whatever junction segment you require.
All It would really require is direction decals added to the block or some other way of knowing which direction is which. Such as another toggle in the info tab to see how the conveyor is behaving.
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