3rd party mail deletion

The limitations that you perceive are not unique to iOS/iPadOS, but are fundamental limitations of using IMAP/POP3 across multiple clients to manage your mail.

The IMAP-service model presumes that the master-copy of your mailbox always resides on the Mail Server - each client downloading a local working copy.

By contrast, POP3 clients simply download email to the local client where it is managed; email is either deleted from the server upon download (i.e., Download & Delete) - or downloaded, leaving a copy in the server server inbox until such time as email messages are moved or deleted.

If you run your own Mail server (such as MS Exchange), you will have far more flexibility in how you manage and organise your email.

The only practical way to acheive what I think you are suggesting is to have a mixed configuration for your iPad and your PC/Mac computer - and have some self discipline in how and when you delete email.

Starting with a PC/Mac - your might consider configuring the Mail client to access your email providers email using POP3. POP3 clients can be configired in one of two main modes; Download and Delete or Download and Leave a Copy on the Server. You will need to configure your POP3 Mail client to the latter.

Whenever your computer Mail client collects mail, it downloads a copy of your inbox to your computer (this being your archive copy). Messages if subsequently moved to local folders, or deleted from the inbox, will be removed from the Server.

Next, for your iPad, you can configure your Mail client for IMAP. Your iPad will remain in-step with the server; as messages are removed from the server, they will be similarly discarded from the iPad.

You should note that in setting Deleted Messages to Never only inhibits automatic deletion of deleted mail items from the deleted email folder of your iPad; this setting does not fully inhibit manual deletion. Your “discipline” comes here - in that you may wish to only delete mail using your computer. If you delete messages from your IMAP-configured iPad, they will cease to be visible to your computer. That said, if your computer has already downloaded a copy, these messages will remain locally stored on your computer.