Speculation regarding this in a nutshell:
Course of Action #1: OF COURSE they would... well, Starscream at least, because he's so prominent and the mold is already there!
Course of Action #2: Not likely, as there has already been a Masterpiece of both these characters... sure, using a different mold, but similar enough to the powers that be at Toys 'r' Us that they don't want to.
Unfortunately, since MP Starscream and Skywarp were Walmart releases, a who lot more of them were produced, apparently, and even though it probably sold well enough, inevitably many went on sale (especially in the case of Skywarp), creating the illusion (or maybe it wasn't an illusion?) of a shelf-warmer.
The fact that TRU had decided on a Masterpiece ACID STORM, of all things, instead of a more prominent character using that mold, seems to point to COA #2, unfortunately...