We do something similar to what you are referring to.
Yes, outputs.conf on the searchhead to forward data to the indexer.
We have an indexapp that contains a local directory with indexes.conf in it. Whenever we add an index we update that file and deploy to all of our indexers and any searchhead who need the index list.
We use a script to "enable" the indexes without restarting the indexers.
echo Enter in Admin password
read pw
for indexer in indexer1 indexer2 indexer3
do
echo $indexer
echo -------------
curl -k -u admin:$pw https://$indexer:8089/servicesNS/admin/indexerbase/configs/conf-indexes/_reload
curl -k -u admin:$pw https://$indexer:8089/services/data/indexes/_reload
echo
sleep 1
done
echo -------------
echo Indexes reloaded
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