You mentioned a wilderness and marine setting. If you think you can envision the possibility of needing these items quickly, in a very bad situation like a heavy storm at sea, then trying to fumble with loading batteries into your laser flare or flashlight, or trying to reverse the batteries or pull out a piece of paper between the cells, could be a real issue. If you're not thinking of situations like that, then there's no harm in simply storing the batteries outside the device.

Some electronics draw a tiny current to keep the electronics powered up, similar to how your TV constantly draws power so it can detect the remote control signal (Unfortunately, I can't imagine life without a TV remote control anymore... ). In that case, keeping the batteries separate might help if you're just going to store the item indefinitely without checking on it. But if you're going to make the habit of swapping the batteries, say, arbitrarily, once a year when you check your PSK, just to be safe, then I wouldn't worry about it and just leave the batteries in the devices. I wouldn't worry about lithium CR123's leaking in your devices in storage.

Some devices also can be turned on accidentally in storage from a bump or shifting around, like in your pack, which means the battery could be drained when you really need it. So, some devices that are easily turned on might require something more drastic like pulling out the cells or putting paper between them. For some things, like some flashlights, you can simply unscrew them a turn or two to prevent electricity from flowing even if switched on accidentally. If you might really need a flashlight in a hurry, carrying it this way would be preferable to reversing a cell or putting paper between the cells IMHO.