The clear tubing level indicator should work fine, although you can kind of see the level of water in translucent tanks anyway - especially if you shine a flashlight into the tank near the bottom. I'm not sure if the flow rate of the pump would be enough to cause it to suck air from the bypass in general - it probably would if the tank is low.
You could put the bypass between the city and gravity fill, then the pump would be out of the picture.
I've never seen a tank with a cleanout hatch - most just sanitize with bleach once or so a season. If you decide to add a hatch, you'd need to position it so your arm (plus a brush?)can reach all the corners of the tank.
I would definitely add a drain as your friend suggests though - it's handy and saves wear and tear on the pump at the end of a trip, plus you can just drain it onto the ground rather than filling your gray/black tanks with clean water.
Good luck!
CC