Exceptions shouldn't be disabled by the toolchain
They're supported by DevkitA64. It should be up to the user whether to disable them.
I generally use the flags forwarded by Switchbrew's template Makefiles to achieve the same build results due to the concerns related to CMake within the community. If a user wants to build with their own flags, they may edit the respective variables. But from general experience, most homebrew developers just copy previously mentioned Makefiles. I feel like having to set the flags they are used to working with introduces a layer of complexity that could be avoided in the most cases.
I stumbled across the same issue. The problem is, as I'm using -DCMAKE_TOOLCHAIN_FILE to use switch-cmake. This prevents my CMakeList.txt files from changing compiler options.
I'm no makefile expert and this was the only way to get it running for me.