Sorry to hear you deleted an important message. I understand how frustrating that can be.
Suggestion #2: The Deleting Messages option should apply to all deletes, including permanently. Alternatively, have a separate option for Deleting Messages Permanently.
I just wanted to tell you about different "delete" commands in Aquamail.
As you've seen already, you have three ways of "deleting" a messages in Aquamail: deleting permanently, moving to "Deleted" folder, hiding on server.
When you choose which one is "default" delete, and that sets the quickly accessible icon for that type of deleting, and the default delete action from the notifications.
But then all three are available to you through the "overflow" (three dots) menu in the message list view. This is for those situations when people want to delete in a way different way than the default one. (For a short while, I had the default option set to "move to deleted" (that's Aquamail default), and then using "delete permanently" for many messages.)
So, you Suggestion #2 does not make sense.
Now, in the message-view (you seem to be referring to that one), the overflow menu (as far as I know) is "dynamic", i.e. the items that appear depend on the options configured, and probably the state of the message.
(Note that your "default" delete option is available for fast access as an icon on the screen. So, there is not reason to repeat it in the menu.)
In my case, - I have "delete permanently" as the default way of deleting. So, I don't have that command in this menu. So, it is hard for me to judge its placement, but Mikeone confirms a similar accidental experience... So, it might be worth thinking about for the developer, Kostya.
Since my delete is configured as "delete permanently", I do use deletion confirmation. For me it is a protection against "fat finger" situations. Additionally, it is a protection against "tumbling" accidents, when I might press the delete button accidentally, while trying to catch the phone as, e.g. it's sliding from some surface. The "undo" option is unlikely to help in those cases.
I've had that configured long before "undo" option became available. (I don't have confirmations for "move to Spam", "move to Archive", as the outcome of those could be reversed.)
I hope this helps you in your understanding of how "delete"s work in Aquamail, so that you can find the optimum configuration and workflow for yourself.
Kostya: IIRC, there was a brief discussion about appearance of that "undo" icon. Maybe this use case warrants that "undo" button to be more obvious (I don't know how to do that short of adding the explicit text). Just thinking out loud.
Also, I agree with the OP that the "delete confirmation = On" is a safer Aquamail default choice, as this case shows. But you have a better vision of users' preferences on a broad scale.