1) Can I use the super size die tray & similar size cutting plastic with the smaller dies?
Yes. You can use a larger tray and cutting plastic with any die. I find it a bit easier to use if the cutting plastic is close to the die size, but it is not necessary.
2) At one time, was there a studio die that cut multiple 3.5 X 6.5 rectangles?
this one cuts four:
http://www.accuquilt.com/shop/studio...multiples.html
this one cuts eight 3.25 X 6.5
http://www.accuquilt.com/shop/studio...multiples.html
If you purchase, I would eventually invest in the Go adaptor. The GO dies usually have fewer repeats on the die and you can cut fewer layers but dies are less expensive. There are some shapes that are only available for the GO.
I've had my cutter for almost 20 years. Let me know if you have any more questions.