It happened to be close to impossible to make standard GNU switches work - defaults for them, that can't be changed at first glance, are not appropriate for us.
Therefore to make it possible to adjust files' locations I've had to add a set of new configure switches.
--with-fbbin executables DIR (PREFIX/bin)
--with-fbsbin system admin executables DIR (PREFIX/bin)
--with-fbconf config files DIR (PREFIX)
--with-fblib object code libraries DIR (PREFIX/lib)
--with-fbinclude C/C++ header files DIR (PREFIXinclude)
--with-fbdoc documentation root DIR (PREFIX/doc)
--with-fbudf UDF DIR (PREFIX/UDF)
--with-fbsample examples DIR (PREFIX/examples)
--with-fbsample-db examples database DIR (PREFIX/examples/empbuild)
--with-fbhelp QLI help DIR (PREFIX/help)
--with-fbintl international DIR (PREFIX/intl)
--with-fbmisc misc DIR (PREFIX/misc)
--with-fbsecure-db security database DIR (PREFIX)
--with-fbmsg message files DIR (PREFIX)
--with-fblog log files DIR (PREFIX)
--with-fbglock guardian lock DIR (PREFIX)
--with-fbplugins plugins DIR (PREFIX)
Also improved ib_util loader to make engine work correctly with new files layout.