The current examples of --prefix=... option usage to point configure script to appropriate depends directory is not standard. This causes some confusion and a bit of inconvenience.
Consider a CentOS 7 32 bit system. Packages libdb4-devel, libdb4-cxx-devel, miniupnpc-devel and zeromq-devel are unavailable from repos. After recommended build with depends:
cd depends
make
cd ..
./autogen.sh
./configure --prefix=$PWD/depends/i686-pc-linux-gnu
make
a user is unable to make install compiled binaries neither locally (to ~/.local) nor system-wide (to /usr/local) as --prefix is set already.
Meanwhile, the standard approach with using config.site files allows both possibilities:
cd depends
make
cd ..
./autogen.sh
CONFIG_SITE=$PWD/depends/i686-pc-linux-gnu/share/config.site ./configure --prefix ~/.local
make
make install
or
CONFIG_SITE=$PWD/depends/i686-pc-linux-gnu/share/config.site ./configure
make
sudo make install # install to /usr/local
Moreover, this approach is used in Gitian descriptors already.