When we've been before they asked us what time we wanted breakfast and gave us vouchers for that time slot to use each day of our visit. Admittedly this was before they started charging for breakfast but I assume it works the same as it did before. Checking in later in the day makes no difference to the time slot you get. We have always checked in around dinner time after a day in the parks and always been able to get the early slot so we can use the extra magic hours. You'd be surprised how many people opt for the later time and miss extra magic hours - not everyone are early birds!
The only thing I would say is that the time you are going might be the main influencing factor. We have always tried to stick with off peak but even going in May it is busy and we were able to get the early breakfast slots. If you are going during peak time then it could be more restrictive if they have given out all the early slots. Then again, we always found there is a never ending line of people coming in and at points seemed to be more people than seats so I am not sure how strict they are with the timings - think the time allocations is more to try and deter a mad rush of everyone in the hotel turning up at once.
I know I rambled a bit but ultimately I do not think it is something you need to worry about too much. But if checking in early and getting your breakfast times sorted sooner gives you peace of mind then do that - it will allow you to then enjoy the parks at least without it lingering at the back of your mind.
Hope that helps!