Hi Jen,
Thank you for this feedback. A couple of quick responses:
In AtoM 2.2+ at least, it appears that 1) already behaves as you wish it to - in my testing, the @identifier attribute in the <eadid> element uses the user-input identifier from the description. If you have reference code inheritance enabled, then it should also include the country and repository codes.
Regarding 3), if you do not wish to have the address information included in your EAD exports, one workaround would be to temporarily delete the address information from your repository record, and then perform any EAD exports required. If you are regularly exporting or trying to automate this process, I understand that this is not practical. However, including this information can be useful for users wishing to migrate their content, or keep it associated with the institution responsible, so I see this as unlikely to change in AtoM. However, it's possible, if there was a strong use case and sponsorship for development, that this might become a user-configurable option in the future?
Point 2) is a good point, and certainly a possibility. However, I'm not sure that adding a number of empty paragraph elements is necessarily a better solution than using the EAD-supported linebreak element. Is there a reason that you prefer this solution?