Interesting, so the 4000CR with CPU would be cheaper for buyers wanting a 68EC030 but I would have thought the percentage wanting a higher end CPU would be growing and decreasing the advantage of adding an unused CPU on the motherboard.
If they wanted a higher end CPU they would buy the A4000/40.
You could argue there would be people who wanted to buy an A4000 without a cpu at all and add a third party one, but that would likely cause issues with people buying one and finding out it wasn't actually a stand alone computer. You'd also likely add more cost by having multiple SKU's. If you are buying an 060 board you can afford the low cost of the EC030 on the board.
It would likely have been cheaper for commodore to only ship the EC030 versions and sell anything faster as dealer upgrades.
Atari banned retailers selling Falcons via mail, unless the customer asked for written permission from Atari that they then passed on to the dealer. That would have severely hampered the uptake, which would have reduced the amount of software being created. It was hard enough for commodore to get developers to make AGA specific games.