the rule-system of almost all email programs is crap, believe me. And the standard use-case is, that you use different devices and email priograms to access your mostly server-side stored emails (imap).
But let me take you to the enterprise side of life:
The right place for rules, white- and blacklists is always the server-side with sieve-rules or even before your email server at your email-gateway. This is where all your emails already exists as files in their corresponding maildir folders. It would be stupidity to transfer these mails to the client and to the server back and forth.
Of course this depends on your infrastructure and to the fact, that you have your own mailserver with your domain and MX nameserver record. This is what I am offering my customers, in recent years mostly kicking ancient Microsoft Exchange Servers by replacing them with Linux Standard Mailservers. See my latest blog post here.
Regarding email deletion: Emails esp. in commerce (invoices, quotes, proposals, contracts etc.) are considered as business documents and companies or business owners (software developers!) have the obligation to keep them for a certain duration. For most documents in Germany this duration lasts 6 years. Your milage may vary but I am sure that tax and financial authorities have similiar rules in your country too.
This is where professional email archieving and quality standards kicks in. In short: Manipulation must be ruled out, every mail must have an index etc. Of course this can’t be done client-side either is expected to do this manually. This is completely done server-side.
So you got an eagle-eye’s view on emails and you may decide, where you are located with your current solution.
Rules in client-side email-programs are toys. it may be okay for private usage, but fails in professional use-cases.