Making a DIY Courier / Messenger bag

Not entirely sure what you are getting at - is this an extra top flap?
Or just raised sides (like Scott's Grobags?)
Also the whole point with a floating liner is that it is only attached around the opening rim of the bag - otherwise as you say water will wick up through the threads and into the bag. Due to the positioning of the flap edges (where the inner is attached) when they are folded over - there shouldnt ever be any part of it where it could get through....

Perhaps some pics/links to examples might help?

What I mean for external flaps is something like the bags used by posties:

http://www.michaellinnell.co.uk/index.php?p=showprod&id=448&cat=Satchels%20and%20Trays

where the flap bends over and keeps close to the sides of the bag. I realise that a flap like that might not be wider than the flap of a messenger bag, just shaped different. I also do not know how well it works. One thing I notice in my bag, a bagaboo workhorse which has the corners of the bag attached to the strap, on the right corner, the one on my hip when wearing the bag, the flap get tightly against the bag when I tighten the strap, while the left corner on my shoulder does not do that, leaving the side more exposed.

About the liner, my bag has a liner that floats off the bottom of the bag, but it is attached for half the length of the side to the top of the bag. Semi-floating then?