--set-section-flags is used to change the section flags (e.g. SHF_ALLOC) for given sections. The flags allowed are the same from the existing --rename-section=.old=.new[,flags] feature.
Additionally, make sure that --set-section-flag cannot be used with --rename-section (either the source or destination), since --rename-section accepts flags. This avoids ambiguity for something like "--rename-section=.foo=.bar,alloc --set-section-flag=.bar,code".