When I modify an organisation I usually make a new Publisher with Metaphorix details in.
I also change the prefix on the publisher to meta, so I can easily tell all the fields I have added.
When you create an organisation CRM automatically creates a publisher called default publisher <name of organisation>
So after I had made my Publisher I would then make a solution and add the entities I would be customizing.
The problem is if you want to use the functionality of using the customization buttons on a form (which you only see if you have the role of System Administrator or System Customizer). If you edit a form and add a field then it uses the default publisher prefix which is new.
I also thought initially changes to entities in my solution would only be recorded if I made them inside my solution but the reality is if you have the account entity in your solution and you edit it using the system customization rather than going through the solution interface then these changes will still be shown in your solution, the only difference is any fields you would have added will have the prefix of new.
well the easy and obvious way around this is to just change the prefix on the default Publisher in your CRM system and then hey presto all your fields will now have the same prefix.