Transactional replication subscriber vs AG secondary replica for reporting
The secondary replica can't be changed inside; and no you can't add indexes. 

You can do subsets and add indexes on the transactional subscriber of something but you will likely encounter issues if you ever need to modify your source tables (such as upgrading the application) or reload data for any other reason; it's good practice to remove it before any change then reapply after and then apply your own changes. 

Also replication often fails for any numbers of reasons. Basically just a warning that it's likely ongoing work and monitoring rather than set and forget. 

For the latter part of your question, you don't have to add it to the AG if you don't want to. I'm not sure what you're getting at.