India and Bangladesh are missing when running on planet.pbf about cosmogony HOT 1 OPEN

Thanks for your feedback.
On which date was generated the planet file you used as the input ?
The most common cause for this kind of issues is that some multipolygons have been broken in OSM. By any chance, do you stll have logs from your run where we could find more details about the boundary parts that would be broken ?

There have been several suspicious edits on India relation recently.
On 2021-03-05 in changeset 100473803, the admin_level value for India has been modified from 2 to 4. That alone may explain why India is no longer considered as a country by Cosmogony.

The diagram from the Wikipedia article refers to former enclaves that have been exchanged in 2015. They are now greatly simplified:

Since the exchange of territory took place, the only remaining enclave is Dahagram–Angarpota, an exclave of Bangladesh.

So the limitations of the algorithm should not be an issue with current boundaries. And this kind of "third-order enclave" should not break the whole polygon anyway.

Boundaries relations with role subarea are not used indeed. But that's actually on purpose. "osm_boudaries_utils" builds a multipolygon by iterating though member ways with role inner or outer. These are the minimum roles that are required to form a valid multipolygon in OSM.
Subareas relations can also be defined as members of the parent relation but they optional and cannot be substituted for member ways. See https://wiki.openstreetmap.org/wiki/Relation:boundary for more details.

from cosmogony.