I reckon the 0mm height clearance. The Z-Axis is usually designed to only move in one direction during printing. You'd probably have problems if it returned to its zero coordinate to print the second object.
Assuming you had two objects, say 8 to 10cm tall, and it prints the objects sequentially as you'd like, the Z-Axis would have to drop to 0cm to start the second object which would cause the X-Axis smooth rods and carriage to foul the first object which is why the printer prints layer by layer instead.
That's my guess.
Why would you need to print the objects sequentially anyway? I'm surprised that it's given as a choice as I can't see the logic in it.
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