The difference with this is wether one is running points in a 1000 or not.
Points-type coils and electronic-type coils are different.
Kettering systems usually have more of everything: turns ratio, primary and secondary resistances, etc. because things happen slower.
Higher resistance in a points-type coil generally limits current draw to keep the points contacts from burning.
Lower resistance in electronic-type coils allows for consistancy. Think of the GM HEI modules. They all have current limiting features that effect and control rise time ensuring that each and every spark is consistantly the same as the next. Things happen quick with electronics, so things happen quick with ignition coils meant for electronic ignitions. Generally, the newer-the quicker. Low resistance coils with 10,000 ohms or more of resistance on the secondary is asking for trouble towards whatever is triggering the input voltage and dealing with the fly-back... Create a bottle-neck and something is going to give. I'm thinking the bottle-neck will show itself in heat. What will give? ...whatever is triggering it.
Unless thought is put through on these swaps the usual route is to put old with the old and new with the new, meaning don't mix a new electronic pick-up with a old point-style coil, or you may burn-up your electronic triggering device, and don't put a new-style coil on a old kettering trigger or you may not get the voltage you were hoping for. Food-for-thought, nothing is set in stone.
So yeah, saturation time is a potential "could be a problem" type of problem. Without specs of the coil, we're shooting blind in the dark. I'm a team player, but... I'm also cautious. When at a loss, I generally don't do what others do just to do it and hope or the best... I need specifications before I tear something up so that I've a valid excuse for spending the money to fix it again.
Smaller is good if it is as-good or better. If it ain't, then it will perform less. If heat becomes a issue because of mis-matched components, then smaller simply is not better.
Again, I think this negative aspect will only apply to 1000's running points. 1100's that are factory with electronic ignitions may see benefit if from nothing else of having a newer coil. Maybe the specs allow for a faster rise time with higher voltage output for a electronic set-up. If it's great for a stock 1100, it just may kill a stock 1000 even with a Dyna "S" trigger.