So, although I received a negative response from Apple (they do not support this in their template parser), I found a way to do this.
I would basically add a new build phase to the template - run script. This woudl script flag indicates the necessary flag files -fno-objc-arc, and then removes itself from the project.
Here is how you can add flags:
PROJ_FILE="${PROJECT_FILE_PATH}/project.pbxproj"
STR_SRCH="\* Class.m \*\/"
STR_RPLC="\* Class.m *\/; settings = {COMPILER_FLAGS = \"-fno-objc-arc\"; };"
sed -i "" "s|${STR_SRCH};|${STR_RPLC}|g" "$PROJ_FILE"
Then, in the same way, you scan the project file and delete the build phase (using the script), so it does not start every time.
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