Finally I was able to make the semantic model work correctly in power bi service by removing the custom connector file (MongoDBAtlasODBC-*****.pqx) on the On Premise Gateway).
Now I no longer have the error "cannot convert Binary Type into into Text type " on Text column containing null value(s).
So it happens that following this documentation is not working in my case.
However I would like to investigate further because this is not the kind of situation we like in production.
Waiting for an explanation if there is one.
Thanks