Is it possible to programatically change Salesforce connectedApp Settings in production in Salesforce?

Hi,

The general rule is that you can't package any settings that would allow granting 'system' permissions. That is, permissions that affect more than just the objects/schema that your package contains.

For example, you can't package CRUD/FLS on Standard Objects and you can't grant System Permissions like ModifyAllData via a Profile or Perm Set that you package. Similarly, any Remote Site Setting that you package can only be deployed into the org in an 'inactive' state via push upgrade or the user needs to explicitly agree to activate it if they do an interactive install.

To your question about Connected Apps -- yes, we had the same problem with a Connected App we package for a Canvas app -- and yes, the admin of the org manually needs to flip the Admin Users are Pre-authorized setting.