gus, if overriding the compiler and specifying special flags for using it is the only problem, we can certainly accommodate that in the current system without the need of a totally new tool chain, hopefully even without too much work.
Several ports have this requirement, in fact, at least for cross compiling. On our buildbot, for example, we typically invoke ScummVM's configure with something like this:
CXX=arm-eabi-gcc \
CXXFLAGS="-isystem /opt/MyCoolSDK/include -fancy-special-compiler-option \
LDFLAGS="-L/opt/MyCoolSDK/lib -fancy-linker-flag" \
./configure --enable-all-engines
This is not pretty, but works, and if this allows us to get the source quicker to SVN, I'd recommend using it (this invocation could even be put into a simple shell script in backends/platforms/android/). A better solution via support code in the configure script is of course nicer on the long run; but this approach sure beats having the whole port source in a separate tree, I think

.
Once again, I'll be happy to try and assist you with this. I don't have an Android phone, nor do I currently have the Android SDK/NDK/whatever setup on my machine (can I do that on OS X?), but at least I know ScummVM pretty well, and working on our Buildbot have some experience with cross compiler setups. So I am quite hopefully we can get that done.