In the post above you say that you are "not concerned about data provider is taking too long to respond.".
Although the /confdConfig/capi/queryTimeout and newSessionTimeout control the timeout for exactly that, i.e. your data provider. The error you get, "couldn't retrieve all data from the data providers, closing session", is due to your data provider applications not responding.
As I wrote in the original post:
See the ConfD developer log with log level set to 'trace' (ConfD side) + your application's libconfd trace log (application side) for details on what is going on with your data provider application.
This will give you a better overview on what is actually going on with your data provider and will give you more details on why the timeout you observe is 3h.