I'm not aware of any flags of C compilers that would "fix potential cache-slot-collisions" for you automatically, neither of any allocators. Intel processors have some profiling registers that can point you to this kind of problems, but typically you first have to know what you want to profile.

Compilers are actually built to align the structures you write as there are a lot of processors which have significantly slower access to the misaligned values. Allocators also have to return you aligned addresses for each "malloc." The newest Intel iX processors are actually an exception in being able to amortize misaligned accesses.

I've actually used hand-made unaligned "string" stores. As soon as you allocate some bigger memory block and store the character sequences of the variable size one after another, their starts won't be aligned unless you want that. For doubles and other fixed-size values it's still better to keep them aligned.

Moreover I wasn't able to extract some value out of the article. Something constructed can be constructed to be slow or fast, fine. But I don't see anything that would inspire me to improve my real code. Maybe somebody who reads the article manages to produce such examples?