I would consider the fab placement in the printer to be of more concern than the pro's and con's of a single foil for top and bottom print.
Do to the larger size of the fab you will have to align the top and bottom layers sequentially on the foil. One in front and one in back. This means you need to consider fab alignment. Are you using the automatic tooling pin alignment in your printer? Will the fab always be placed forward in the printer or are you intending to print the second side with the fab placed far to the back? This would necessitate moving the fab supports and vacuum boxes. It would be better to leave the fab forward, regardless of which side is up and rotating the stencil 180 degrees between runs. This also forces the centerline of each stencil to remain true and in alignment with each other. Can you rotate the stencil frame and achieve center alignment?
One final thought - why do 2 on 1 anyway? Are you trying to save the cost of one stencil? What if you find that one of the two aperture sets needs to be modified? That means you will need to get both sets cut again rather than one. Is your stencil house charging a flat rate, regardless of quantity of apertures? Or is the charge proportioned by aperture count? Are these laser cut or chemical etch stencils? If chemical etch, I would be wary of good center line alignment between the two sides.
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