Is there a reason why "Môr" is sea and ocean instead of having separate words like in english?
there are two separate words. It's just that they call the various oceans and seas in the world ''mor''
Why is "y" after "Môr" here, but before "Môr" for "y Môr Tawel," etc?
They are just the conventional names used for the various oceans etc. I don't think there is a particular reason. Bear in mind that Modern Welsh has been around for a few hundred years now, so quite a few 'reasons' for things being the way they are lost to most of us.