Answering your questions:

Should the message sizes in the message list be placed somewhere else?

In my opinion, yes, as it reduces the subject line length, especially on small screens. However, I couldn't find a better place for this. Maybe it could be added below the date and above the star, but I'm uncertain about how it would look in the end.
Perhaps @laurelterlesky has more suitable advice.

Should the message size be also shown when a message is opened? If yes, where?

I would really appreciate that and would even suggest it. When you open the message and tap on the header, a bottom sheet should appear with the message details. I would include the information there or/and in the header itself. Since this involves design, I would also like to see if @laurelterlesky has any more suitable suggestions.

Should displaying the message size be enabled by default?

I don't believe we should. While this feature is nice, I haven't seen it often in other email clients, and I'm unsure if all users would want that information displayed without their consent. Moreover, it adds extra information to the message list, which could be distracting for some users. Therefore, I would prefer to keep the default setting as false.

Is the description for the message size display toggle setting alright?

If you add the size information also in the Message Preview, I would change just a bit the end, removing the "list" from "message list". Otherwise, it is a good description!

Should we use 1000 or 1024 as base for the sizes? So KB, MB, GB vs KiB, MiB, GiB?

There is a SizeFormatter class that already handles that. We should use it to keep consistency.

Is the schema migration alright?

Ideally, during the migration process, we should provide the correct size for each message when adding the column. However, I'm not sure how to accomplish that.

What concerns me the most is seeing many instances of "0B" associated with my messages, which suggests that something might be wrong with them.

I would prefer to leave the messages without a calculated size as NULL and hide the size label in these cases. The label should only be displayed once the size has been properly calculated.

Perhaps @wmontwe knows better how to recalculate the current stored messages' size.