Keep in mind I am not an expert on alignments. I have done a crapload of car work that needed them after though, and have been really disappointed over the years with how many times I had to repeatably bring cars back that pulled or had an off center steering wheel afterwards. So I got the Gyraline setup to do it myself. Which has worked perfect the 10 or so times I've used it. I was also tired of paying $100 every time to get them done badly.
You don't need to use any body reference if you are just doing a simple alignment, only if you want to make sure your car isn't tweaked somehow or if you have done something really major to the front or rear suspension that is adjustable after. It shows all four tires compared to each other normally. Like if the front tires are correctly spaced but both pointing right or left compared to the rear when your steering wheel is centered you know you need to adjust them both the same amount/direction to center them to the steering wheel.
You would want to buy or make something to hold the steering wheel centered during your adjustments, or on a older/project car just leave/take it off and put it on centered when done.
I removed the front steering, suspension, and brakes from my 67 Cougar and replaced it all and modified some stuff so I used the app to get everything right to the car, then put the steering wheel back on centered. It tracks beautifully and has shown no sign of weird tire wear or anything. I used a body line for reference but honestly I am not sure anything on a car that old is really square. Using a referance was also good when I changed the rear leaf springs, I used it to get the axle square to the body and front tires when bolting it all back togather and used a tape measure from the frame to make sure it was centered at the same time.
If you had really clean spots on the frame rail for the two small contact points to touch and you thought the frame was square you could use that, but any undercoating or dirt is going to throw you off. We are taking about about .005 of an inch, so your frame contact points would need to be very clean and flat to do it well.
For your project its not going to show you if your axle is centered, only if its angled. So you would have to measure that separately, which I wouldn't think would be hard to do. If you were dropping the body on you could check to make sure it was square to the frame, but it would not show you if you had it to far forward or back, only if it was angled compared to everything else. As far as I know it doesn't show any distance type measurements, just measures angles.
Also you can switch between degrees, inches, or mm at anytime before, during, or after you take measurements which is great because if you tell me I need to adjust a tire by 2 degrees it aint happening, but if you say 1/8" I'm all over it. Most specs are in degrees so its great being able to go back and forth.
Not sure if that all answers your questions properly, let me know if you need something else or want me to try anything with mine. It has a handy screenshot button so I could get screenshot/s of something if you wanted.
Here are some of the different measurement screens and one where I was messing around with it at my desk. The little line with the specs on that one is the spec for the car you are measuring, it has a database where you can find and add cars, or make a custom one like I did for my Cougar becouse I am not using the stock settings-




The one where I was messing around and some settings screens-


