Just to add my 2 cents, - I see in my use of Aquamail how both ways are important for me in different situations.
If I am trying to zoom in while trying to read some illegible portion of the messages (especially if it is HTML-formatted, and has some tiny font portion, or when there is an image), I'd indeed prefer for the focus to remain in the same part of the message.
However, if I just want to read the entire message zoomed in (due to a combination of several factors: tiny font throughout the message, my eyes are tired, and I don't have reading glasses), - then I'd prefer it to be reflowed, as it is annoying to scroll it horizontally for each line.
So, I think both options are important.
Moreover, in a perfect world, I'd prefer to have a quick-access toggle-switch button on the screen in the message view after zooming in: "re-flow/do not reflow". But given the fact that it takes the valuable real estate and that this switching is not needed too frequently (that's for me so far, - some people may need it, - or I might need it when my vision worsens) by many enough users - I would not expect or even really propose to have that toggle switch on the screen, but just in the settings.