It seems to me there's a build/target mistake in the Makefile. sqlite3 is built for the target, not the buildhost, right?
Thomas --- Makefile.in.cc 2016-01-21 12:58:26.251338551 +0100 +++ Makefile.in 2016-01-21 12:58:46.044901935 +0100 @@ -1169,10 +1169,10 @@ lib_install: libsqlite3.la $(INSTALL) -d $(DESTDIR)$(libdir) $(LTINSTALL) libsqlite3.la $(DESTDIR)$(libdir) - -install: sqlite3$(BEXE) lib_install sqlite3.h sqlite3.pc ${HAVE_TCL:1=tcl_install} + +install: sqlite3$(TEXE) lib_install sqlite3.h sqlite3.pc ${HAVE_TCL:1=tcl_install} $(INSTALL) -d $(DESTDIR)$(bindir) - $(LTINSTALL) sqlite3$(BEXE) $(DESTDIR)$(bindir) + $(LTINSTALL) sqlite3$(TEXE) $(DESTDIR)$(bindir) $(INSTALL) -d $(DESTDIR)$(includedir) $(INSTALL) -m 0644 sqlite3.h $(DESTDIR)$(includedir) $(INSTALL) -m 0644 $(TOP)/src/sqlite3ext.h $(DESTDIR)$(includedir)