I think the TFwiki article "To Sell Toys" best answers that.
Like Bumblebee and Starscream started wearing bodies that look like the WFC bodies but those are new forms as far as IDW continuty is concerned, not reversions to their forms that the Aligned Bumblebee and Starscream in had at the start of the war. So you could use those to represent the characters in WFC, or as the pre-Earth forms of TF Prime Bumblebee and Starscream, or as post-war forms of G1/IDW Bumblebee and Starscream.
The question is really if the new IDW based toys are "Aligned" or not. I'd argue no but who knows what Hasbro would say. I'd say "Generations" gives any toy in that line the flexibility to be a character from any continuity.