The detection of features such as STL or SQLite by checking files under \epoc32\ does not work in clean builds (which start with an unpopulated \epoc32\ source tree), e.g. this code will not detect the STL properly:

exists($${EPOCROOT}epoc32/include/stdapis/stlportv5) {
OS_LAYER_STDCPP_SYSTEMINCLUDE = $$OS_LAYER_PUBLIC_EXPORT_PATH(stdapis/stlportv5)
} else {
OS_LAYER_STDCPP_SYSTEMINCLUDE = $$OS_LAYER_PUBLIC_EXPORT_PATH(stdapis/stlport)
}

and this code will not find SQLite:

!exists($${EPOCROOT}epoc32/release/armv5/lib/sqlite3.dso) {
BLD_INF_RULES.prj_exports += ":zip SQLite3_v9.2.zip"
}

One solution could be to use explicit configure parameters to either override the autodetected state, or to use the feature manager for detecting the configuration. The simpler solution of using configure flags is probably faster and makes definitely sense here.