What about clipping a strobe to the liftbag if it's an emergency? Whenever I'm boat diving, I carry a Princeton-Tec Aqua Strobe (the 1AA size). It's on a bolt snap - the Halcyon bags have a small SS D-ring on top of them, if it was an emergency where you did have time to shoot a bag, what would be wrong with clipping the strobe to the top of the bag before shooting it? Granted, the strobe would probably not be very effective in bright sunlight, and would tip the bag over to one side, but most boats have binoculars on board - surely it would show up if a crew member looked at the bag through a pair, or at least the body of the strobe light itself would be visible. And it would certainly make the bag more visible on late afternoon/dusk/night dives.
Bag with no strobe attached = practice shoot, or drift deco
Bag with strobe attached = come and get me
Again, pre-dive briefing should cover this. On the occasions where I've planned a practice bag shoot, we inform the boat crew that we are planning one, and that no action should be taken. But then I've always wondered what would happen if we did get seperated from the boat, they see our lift bag, and ignore it because we told them to!
This would save having to carry two bags (although colors could be split between divers in a team), and a strobe is a valuable boat diving tool that you probably should carry anyway.