The OP asked if it can be done, and the current system does not do it.
The case is similar, but not the same. There's important differences. A misread
of a real cart could result in a brick if they went the route you're talking about, but that's risky which is why Nintendo chose to go the current route. Note that both flash carts
and misreads of real carts produce the same error from the console (which tells the user to refer to the manual, which gives generic help messages that don't even mention flash carts or piracy). This points out that giving a generic error is
a conscious design decision by Nintendo, and there's some precedent as well. In
the gameboy boot sequence, some static data is read from the cart (the Nintendo logo), and if the data is malformed the system locks up instead of going on to read and possibly run corrupt data. In addition to not allowing carts with modified data to boot, this can save the user headaches such as games corrupting or erasing their save data if the gameboy starts reading and then executing bad instructions.
On a technical level there's quite a difference in risk associated with modifying firmware versus using a third-part accessory (which a flash cart is). How many people do we see bricking their PSPs by modifying flash0 and touching other stuff they don't need to? Lots, and they have themselves to blame, Sony has no obligation to help them because they're the ones that messed the system up
with unauthorized modification of the unit itself. How many people do we see bricking their DSi and 3DS units by modifying the internal software? None, it doesn't happen. The unit itself is never modified, that's the important distinction.
"Well
if things were different they could brick it." Yes, and
if Scar helped Mufasa up the clif instead of throwing him off in The Lion King, the movie would turn out differently, duh... but that's not how it is.
