I didn't know there was such a thing as a tower-only accelerator for the A1200, or I would have specified that when I ordered it.
There isn't such a thing, but some accelerators is recommended to be used in a tower case, for instance the Apollo 1240 you have. As you have already discovered, it works fine with your A1200 desktop, the computer just can't be reassembled.
I'm tempted to hack some off the top of the SIMM socket with a hot knife, and bend the matal clips back enough so that the keyboard and case can be reassembled. I think the SIMM socket might still be usable down the road, even if it required using a rubber band or zip tie to hold a SIMM in the socket.
If I were you, I wouldn't do that. You dramatically reduce the price of the card if you plan on selling it, and you end up with a machine you aren't satified with (the 040 card generate a lot of heat, which means that the A1200 often needs to be raised above the table, making it unstable again, depending on how you raise the computer).
If it was me, I would bite the bullet, and sell the card with a loss, and go for a Blizzard 030 card instead. It generates less heat, fits the trapdoor perfectly, you can reassemble the case, can take up to 128 MB of ram, etc. If you want more horsepower you can go for a 060 card.
Maybe someone would like to trade their Blizzard 1240 for your Apollo 040?