The currnent way basedir works is a bit undesirable, especially when one wants to build FHS compatible packages.
See for example the madness that debian does in order to get SKS FHS compatible, thereby making -basedir basically useless.
IMHO the concept of basedir is anyway wrong, SKS should either allow to specify all the locations manually (i.e. command line switches for the /etc/sks dir, /var/log/sks dir, /var/lib/sks dir, etc.) or even better (and as most projects do) hard compile this and make it configurable via the build system.
In both cases, -basedir would probably go away.