Indexing in all non-internal indexes counts against the license, except for summary indexing which is 'free'.
Non-internal indexes are generally the ones not starting with an underscore when you look at a fresh Splunk installation (that is, you can't create your own index with a leading underscore and get free indexing there 😉 )
Hopefully someone from Splunk can chime in with an authoritative answer here.
My guess would be that internal status of indexes is hardcoded, otherwise it would be all too easy to give yourself free indexing.
Obvious next question .....
What makes an internal index internal ? 🙂 Is it hardcoded in the binary ?
Do any add-ons ship with extra internal indexes ?
While, isInternal is exposed in
https://localhost:8089/servicesNS/nobody/search/data/indexes/
there's no setter function in the POST.
Academic research only of course...