the reason it says selected portion because you can create un-managed solution and only add one entity for example account and when this solution is exported relevant customization xml will only contains customization and configuration for account
entity only and not entire entities of CRM.
RibbonDiff changes are configuration since based on your ribbon diff commands system generates relevant ribbon button and yes you are right it is better to use third party tool to do ribbon changes. in my experience tool is good enough in most scenario but
there would be scenarios where you had to directly change customization XML
Hope this helps
MayankP
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