First, Let me tell you the difference between Primary Field and Primary Key.
The Primary Key for account is accountid.
The Primary Field for account is name.
All Microsoft dynamics entities has unique identifier known as GUID, which we call as Primary Key of a particular record and it will always be there for each entity. You cannot create your custom Primary Key, the Key you creates is actually an Alternate Key, not the Primary Key.
Prior to Microsoft Dynamic CRM 2015 Update 1 the only way to identify the records in CRM was the record guid. Now with the introduction of the Alternate Keys in Dynamics CRM 2015 Update 1 we can use alternate keys to uniquely identify a record in CRM in place of the primary key (GUID).
Alternate Keys are there to help you keep your records unique based on the other fields.
For example:
Inside Contact Entity you add a field to store the Aadhaar (the Indian Identification Number) and set it as Alternate Key, in this way you can't save two contacts with the same Aadhaar.
Answer of your 2nd Ques - Dynamic CRM uses only Primary Field in order to make relationships with other entities.
Answer of your 3rd Ques - No, it won't. Because you cannot replace the CRM default Primary Key. The custom Key you creates is the Alternative Keys as I explained earlier.
Hope you get the understanding now.
I would recommend you go through the following articles to get to know more about the Keys Concepts:
https://www.inogic.com/blog/2015/04/more-ways-to-search-a-record-in-dynamics-crm-2015-update-1-alternate-keys/
https://community.dynamics.com/crm/f/117/t/215343
https://www.powerobjects.com/2015/08/21/utilizing-alternate-keys-in-dynamics-crm-integrations/
https://blogs.msdn.microsoft.com/crm/2007/06/18/understanding-crm-metadata-primarykey-and-primaryfield/
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Cheers
Arpit
https://arpitmscrmhunt.blogspot.in