Protocol buffers is heavily scrutinized and as for Boost, the way it's designed means that it only pulls in what you use. The project seem to only use very little of Boost anyway, so I wouldn't bother too much about it.
More surprising, I can see it does not use Boost.Asio for networking (strange ?). It seems to use Boost for things like Boost.Lambda (deprecated with C++11) and typeof.
I think the project could benefit from leveraging the Boost libraries more or just not use them at all.
Examples: use Boost.Spirit for Base64 and replace the custom made parser. Don't use malloc to allocate raw pointers but use strings, vectors or smart pointers. Replace the networking code with Boost.Asio (which is portable). etc.