GagnonAlexandreNC-2861, I'd been discussing on this internally with our product team.
Currently, this is not supported out of the box. In order to orchestrate something similar -check the following approach:
If your requirement fits and you're fine to to modify the code to point to specific folder. You may keep an Azure Table of all documents metadata (including location) and use a custom skill from a single indexer.
Kindly take a look at the sample on how to move blob metadata from Blob Storage to Azure Table (in batch for initial ingestion and event-based to keep it up to date when new blobs are created or deleted), and how to use the Document Extraction skill to crack documents with a custom generated SAS Token.
Sample from one of our PG team member: https://github.com/ruoccofabrizio/azure-cognitive-search-multiple-containers-indexer
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Much appreciate your feedback! Thanks for your patience!