First off...Congratulations on the new kitten
Bless you for being Scruffy's angels.
Half of my tribe are males, and to be totally honest. The males get along FAR better than the females do. I will often find all of them sleeping in a pile, while all the girls have their preferred spots.
All very good questions....I doubt that Buffy really has any plans to hurt Scruffy. It's just one male cat setting the ground rules to another..."if you're gonna live in my house, there are some rules....."
Eating from the same bowl is fine, IF they will do it, and it has to be up to them. As for littler boxes, only time will tell. There are 8 cats here, but only 6 litter boxes. Over time, I would remove the one that they didn't or barely used. But it took a couple years to make that determination. Sometimes they would use the odd boxes because I had just cleaned them. Sooo, I started cleaning the little used boxes last, while they were busy with their freshly cleaned favorites. After a while it was obvious that they didn't care for the other two, and I took them up.
Again, congratulations on the new furkid, I'm sure that he and Buffy will be acting like brothers in no time.
Oh, and there may be fights, but it could also be rough playing. Sometimes Trace and Mischief with fight and scream and anyone listening would be sure that this house isn't big enough for both of them...but then they will stop in mid-wrestle to clean each others ears. My boys are clowns....