You can't, aside from adapting the sources and recompiling. I'm in a mood to do a rewrite of it soon, though. I'll have that on my list then. I'll probably migrate to implement much of the blitting in LuaJIT/FFI, so that would be highly scriptable. Another plan is to make it usable on the Kobo, too. I'll also implement the proper ioctl for newer devices' (K5, KPW) eink updates, so that awful "eips" loop can go away.
As for update regions and speed: That's a function of the RFB *server*. It is responsible for sending updated framebuffer regions. So my suggestion is to try those out a bit. Same for CPU usage: E.g. on a USB link, it doesn't make much sense to instruct client and server to use sophisticated compression algorithms for the tiles send back and forth. No good documentation at the moment, but kindlevncviewer hands its parameters down to this function of libvncclient:
http://libvncserver.sourceforge.net/...44eb97d2356475 - there's the "-encoding" parameter to try out.