How can I change the messages in the channel window to flow from the top down (as they do in Pirch)?

You can't, at lest i never seen that in mirc.

Realistically you can't, but technically you could use a script that transfers the text to a custom window where the most recent line received is inserted at the top.

What's the point? When the channel window gets full in pirch the next messages appear at the bottom (same as mirc).