I noticed the exhaust manifold has more rust on it compared to a 2004 Civic. The 2016 ILX has a little over 100 miles but did sit on the dealer's lot for over a year. There's also a good deal more rust on the side engine mount compared to the 2004 Civic. I also took a picture of a hose that looks like it has a lot of water mineral build up stuck on it. All of the other hoses are completely clean. Is that amount of rust normal for a 1 year old car?

 

It looks like surface rust to me. Since it is a newer car, you may want to look at another ILX on the dealer lot to see if it is a common problem.

I grew up in the northeast where they salt the road, so that is not excessive rust to me. Since it is a new car, you could see if a dealership would do anything about it.

If it were my car, I'd clean up the rust with steel wool, then use that rustoleum rust converter on an acid-free brush to prevent it from returning on the motor mount. Not sure how the rustoleum stands up to heat, but you could try it on a spot of the manifold.

Can't tell what that hose is connected to, but it looks like brake fluid. Maybe dirty water splashed up on there from under the car. Just clean it off and keep an eye on it.

 

I'd think it's more of a difference in how the metal was made (alloy mixture for the steel/cast iron).
I live in the "salt belt" and we see real rust here (not like what your photos show), and I have some rusty cars sitting here to prove it.

 

First World Problems...