Own answer:
Create a script reset.sh
like:
grep -E -h -v '^(#.*)?$' $@ | sed -E 's/(.*)=.*/\1/; s/^(un)?set/reset/g; /macro/d'
and as Adam suggested, in the main conf:
set my_reset_source=`~/.mutt/reset.sh ~/.mutt/*.config > /tmp/mutt-reset`
folder-hook . source /tmp/mutt-reset
folder-hook home source ~/.mutt/home.config
folder-hook work source ~/.mutt/work.config