The memory returned from malloc() that you will assign to a pointer to the struct with the zero-length array member will be aligned memory ... that's required by the C99 specification. So there is no issue overlaying a struct with a zero-length array over memory allocated from the heap via malloc().
Where you would run into trouble would be attempting to overlay your struct over some raw buffer in memory that came from a packed or non-traditionally aligned data-source, such as a file-header, memory-mapped hardware interface, etc. In those cases, using a zero-length array to handle the variable-length data can be a bad idea since the data may not be aligned according to the default alignment parameters of the platform, and thus offsetting into the array will not yield the correct results.
