How far in advance do I need to arrive at train stations to be on time?

1. There is security. Liquids are fine; it is not as extensive as like an airport just an xray of the bag. You can buy coffee on the train if no shops are open.
2. The security does not take long and flows a lot faster than the airport; every bag just goes through the xray.
   

I arrive 30-45 minutes before departure.

Security is really minimal, basically you wait in line, when you get to the front, toss your bag on the conveyor, pick it up on the other side. No metal detector or scanner for you, you might be asked to take off a jacket, but that is about it. Food, drink, and most anything else you pack is not a problem.

The train station will be the most likely to have something open, Google indicates some of the food places open sometime between 5 and 6.

If you are not familiar with Atocha, then allow 45 minutes or more, If you have it down pat, 30 minutes is fine. Though be warned, they did start construction on some areas, expected to last a while, so that could warrant a bit of extra time.

The coffee shops/snacks/groceries will be in the main terminal area. There is nothing on the platform. In Spain access to the platform is limited to tickets holders and (I think) fifteen minutes prior. There is light security check -- hard to hijack a train and a briefcase size bomb isn't going to do much damage. No limitation on water bottles, food, size of suitcases, etc. We have had a couple bottles of wine with no question.

I'm sure there was a scanner in Chamartin station last year, because they took away the scissor I always bring to wrap packages. Imagine there must be one in Atocha as well.

Security is pretty fast but the stations are large, so keep that in mind, especially for Atocha.

Depending on the class you booked on IRYO, they might provide breakfast and drinks. I know they offer these on their Infinita Bistro class, and the food is not bad at all.

At Madrid Atocha there is general security (procedures as described above) for everybody accessing the departures area. You then wait there until they call the gate/exit number and just show your ticket. The procedure to go to Toledo is the same.
Sevilla is slightly different because you wait in the station hall until they indicate your gate, then queue there, show the ticket, go through security on the platform or just before and then directly onto the train.

Arriving 45 minutes to an hour at Atocha–Almudena should be plenty of time. Less if you know exactly where you are going and you are traveling light. Getting food either at the train station or on the train is not a problem. In fact I buy the first class tickets with food included when I can. Sandwiches from the train station are better than the ones at the cafeteria car on the train.

The security is purely for show.

When I took trains last spring I noticed something interesting: Queues would form at the entrances to the platform about half an hour before departure. They would then start checking tickets about 20 minutes before the train was due, and the queue would be gone by T -10 minutes. So I just sat at the little bar, drinking my coffee, then at T-8 strolled over to the gate, showed my ticket, walked down the stairs and boarded the train. Given that everyone has a reserved seat I do not understand why people queue. But maybe Spaniards have forgotten what it is to take a train...

Last time we tried to take a train in Spain, was Barcelona. We wanted to visit the nearby city that was once the regional Roman capital, forgotten the name. We got to the station about 45 minutes (didn't have our tickets). This was over 10 years ago and the ticket machines wouldn't take our credit cards, so we had to stand in line to buy our tickets.
After half an hour, the line hardly moved at all, so we gave it up and left the station.

WengenK described our experience perfectly. Several years ago Spain had a bomb exploded in one of its commuter trains so the platform screening is the results. Actually it makes it pretty safe. Not many pickpockets on the platform willing to help you handle your luggage.

We just did some of this, this week. I am risk adverse so left our Madrid hotel at 5:30 for a 7 am train. You can board about 30 minutes early.
I was concerned about luggage storage which was not a problem Madrid to Seville. There is a lot of construction in and around the station.
You can bring food. We had quite the picnic earlier in the week Barcelona to Madrid during a mid day train that we bought at the market.

From Seville back to Madrid we left our hotel around 5:45 for a 7 pm train. Here our train did not have great luggage storage and if we were not one of the first ones on the train it would have been a problem.

We did have extra time and probably could have left later but as I mentioned I am risk adverse. Enjoy your trip