With trunk G++:

$ ~/gcc/bin/g++ --version
g++ (GCC) 4.6.0 20100901 (experimental)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ cat fdc.cc
extern void cf();

// no warning
void *f() { return __extension__ (void *) cf; }

// warning:
// ISO C++ forbids casting between pointer-to-function and pointer-to-object
template<bool flag>
void *ft() { return __extension__ (void *) cf; }

template void *ft<true>();
$ LD_LIBRARY_PATH=$HOME/gcc/lib ~/gcc/bin/g++ -Wall -pedantic -c fdc.cc
fdc.cc: In function ‘void* ft() [with bool flag = true]’:
fdc.cc:11:25:   instantiated from here
fdc.cc:9:44: warning: ISO C++ forbids casting between pointer-to-function and pointer-to-object [enabled by default]

I would expect G++ to either complain about both casts, or neither; whether the code appears in a function template shouldn't matter.