The memory in question here is RAM, not SSD (permanent storage space).
Any decent OS should be able to protect its own processes from user-level operations. Any decent OS should also be able to assign a block of memory for its own use so no user applications could mess with it.
And I hope the iPhone OS is a decent OS...
Obviously Apple could have had iPhone OS work this way if they wanted it to - and I'm sure it does in fact work this way for truly essential processes - but the iPhone is not a desktop computer with gigabytes of RAM. Apple's approach is to try to keep Safari, etc. in RAM as long as possible so that they always re-launch as quickly as possible. However, if one particular app is facing a critically low memory situation, Apple is polite and will kill its own apps to try to keep the foreground app alive.
The free memory apps work by flooding RAM with random data until there is so little free memory left that Apple politely kills its own apps, freeing their memory. Then the free memory app frees all of the garbage data it puts in RAM and voila, most of your RAM is free.
I am surprised that Apple didn't pull these apps a long time ago seeing how they undermine Apple's desire to keep Safari, etc. in RAM unless it's absolutely necessary not to.