This is how it's always been, and is unlikely to change. The 75% discount to factories doesn't apply until it is put in the build queue, and to be honest I'm not sure it'd be worth the coding time to fix it so that it is applied before then.
My only question is if you can play around this like all of the rest of us have been doing or if it necessitates fixing in your opinion.
As a note, the 75% discount is to base cost, so you won't see a 75% discount in the rush buy cost (in fact in most cases you'll see more). Rush buy cost = base cost ^ 1.1 (truncated) * 6. Of course, the game factors in the cost (or social production spent, whichever is greater) of the previous improvement on the tile (or rather, that which has not already been given credit for), so your values may not always appear to work with that formula, even though it is accurate.
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