I don’t think the power levels are scaled; Bonkle characters have a myriad of elemental and mask powers, while the inhabitants of Middle Earth have their steel (or mithril) and a handful of magic powers, and I believe that most of these powers aren’t offensive.
In scenario #2, the Makuta would absolutely crush Middle Earth. Like Sauron and Saruman’s forces they could field massive artificial armies, which put the heroes on the ropes in most battles, but their creations would have Kraata and Rhotuka powers. Plus, they could create lots of war Rahi.
Scenario #1 would be a little more balanced, I think, in part due to the nature of the heroes and in part because of the exact nature of the scenario you described. It would be a race against time because Mata Nui is dying at the time, and the Inika still have to deal with the Piraka and Brutaka. Also, depending on the nature of the transformation, the Mask of Life might not be in the Matoran universe anymore - if so, the Mask of Life would kill everyone within the Matoran Universe. Sauron’s forces would be strategically placed outside the Matoran universe, on Voya Nui, so if they could overcome the Toa Inika they would be able to conquer it and the at-the-time uninhabited Mata Nui, but it would be a rather hollow victory.
I would disagree. The Makuta created the Rahi, thus their ability to control them. They didn’t create the creatures of Middle-Earth, who are fully biological and weren’t developed by Makuta virus.