yes, message handling needs to fit in many requirements to get it right properly. I’ll try to explain how what you require would work based to the functional design devised here (lower level description) [1,2].
New and current messages are planned to get synced between all email(-chat) clients, by default. This for example allows deleting a message on one device, without having to delete it again on all other devices.
If there is not enough space on the server, deltachat is required to automatically delete messages from the server to continue to function (for a minimal solution). But there is the “archived message” feature that will allow deltachat to keep messages on the local devices, independently from what happens on the server. The clients may then auto-archive, if that removes the message from the server.
There would then not be much need to do what you wrote above (manually delete on server), because deltachat would automatically ensure to keep enough free space on the server, while keeping local archives. But it would be possible to delete for example spam from the server, and get that removed from all deltachat clients as well.
Also see the forum thread under "Clear chat" function that contains some relevant explanations and example cases.
 [Wiki] Use-cases, chat rules and configuration options
 [Wiki] IMAP strategy to chat within the email ecosystem