tools: Allocate the priv structs with proper alignment

Previously, they could be allocated with any random alignment
matching the end of the MuxerContext/DemuxerContext. The
priv structs themselves can have members that require specific
alignment, or at least the default alignment of malloc()/calloc()
(which is sufficient for native types such as uint64_t and
doubles).

This fixes crashes in some arm builds, where GCC (correctly) wants
to use 64 bit aligned stores to write to MD5Context.