The windows on the turtle are not that bad, you just need to know which spots are safe. Also, destroy the pillows on the floor with a crowbar (Mr. handy) to have faster walking.
Safe spots are the six tiles at the rear exit. On the side door, there is one safe tile. It's right at the door, next to the wall of the cabin. My other soldiers are usually then in the area opposite to the side door. Not optimal, but when you remove the pillows for faster walking it's manageable. You first go out the back and look to the right to check if someone is standing in a position to fire into the craft through the side window. If there is, don't move anyone through the danger area.
Windows are not only a disadvantage. When using the seductress outfit the windows are quite useful.
Special mention for the start of battle: How to safely get your crew out of the cockpit into the main cabin.
Face the window. Walk 1 tile at a time while holding your "run" key. This will make them sidestep, meaning you walk a tile, but you don't change the direction you look at. This will prevent enemies reaction firing at you, because of the rule of mutual surprise. If you get vision of the enemy at the same time as he gets vision on you, he doesn't get a reaction shot (for this one tile you walked).
If you can see the enemy, this is 100% safe if done correctly. If you face enemies you cannot see due to night mission or them having camo, then you are out of luck.
Regarding the shadowbat: yep, it's safer than the turtle. Only risk is sniper/spotter enemies throwing grenades into the craft through the hatches in the wings. So depending on the enemy it has unsafe tiles as well that you need to avoid standing on.
