Has there been any discussion of adding `getUtxosByCovenantId`?

Hello and welcome. This is a good and relevant question.
As far as I know, this is a RPC that is planned to be develop.

I would argue though that your concerns are exaggerated. You are correct to note that there is a need for a per-app indexer, this does not mean though that the d-app FE must trust it blindly. A frontend of a dapp could easily validate the truthfulness of the information provided by the indexer.

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