If you have an app feeding you solutions based on a 100 yard zero then that is the obvious choice.

Personally, I tend to zero most rifles closet to 200 though. Usually that is pretty close to giving you maximum point blank range -- ie anything inside of about 250 won't require any adjustment at all with that setup, but with a 100 yard zero you will have to dial even at 200.

There is nothing really special about the mil system. 3.43 mils is one MOA. It's kind of like measuring in meters vs yards, but for angles -- you're just using different units.

MOA is often thought of in terms of inches per hundred yards. This works well at close range, though it's actually about 1.047 inches per 100 yards, and this error becomes significant at longer ranges. The main convenience here though is if you measure ranges in yards and are close enough that your adjustments will be measured in inches.

1 MIL is 3.6 inches at 100 yards. The trick here is to notice that 100 yards is 3600 inches. There is the beauty of the MIL system -- one MIL of distance on the scope is marking out 1/1000 of the distance to the target. Looking at something at 100 feet? Those dots are 0.1 feet apart on the target. 1000 meters? Dots are 1 meter apart.

Either way though, if you are making adjustments for wind, or otherwise looking at point if impact and adjusting through your scope, it's helpful to not think about units or even ranges very much. You have dots in the scope. You have clicks in the turrets. Equate one to the other -- this many clicks equals this many dots. This applies no matter what units the angles are measured in.