Can I use multiple shades of the "Two Colors"?
Hey! Thanks for joining! Technically, no. Another shade would be considered another discrete color in this case. However, you're being graded on "bitness" (meaning how well you kept to the specification) , so your game will still be accepted with multiple tones, but it will likely suffer in the primary scoring category.
we did it in Aspect Arcade (some of the particles fade out). imo it's really more of a grading risk than anything, as you're being graded on Bitness -- in other words how 1bit your game is -- so in a sense it's up to your fellow competitors if they accept alpha values as allowed. Bitness is ultimately just 1 of the scoring categories.
but, to more directly answer your question, alpha manipulation would break the "1 bit" rule.