Could you just ask him what he'd rather read? (that's a serious question, no sarcasm). If you want to go the original pilot route just maybe a polite letter of "Hey, I know different showrunners have different preferences. I have a spec of X show or a pilot about X, which would you prefer?"

But if you don't want to do that here's my two cents from having interacted with staffed writers and showrunners.

If it's a show that recently went off the air (like the series finale aired this year) submit that script. Otherwise find a show that is similar to the one you want to get staffed on and write a spec for that.

Do not submit a spec for his show. The showrunner is so deep into their show he'll only see what's wrong with your spec...plus there may be legal issues with that.

There's been a shift toward pilots (Personally have heard arguments for and against this) but ultimately what this showrunner is looking for in reading your work is two skills:
1.) Can you write in the genre of the show (i.e. if this is comedy. Are you funny?)
2.) Can you mimic the voice of a show that isn't yours?
An original pilot can be a nice sample but it speaks nothing of your ability to adapt and capture the voice of an existing show (which is essentially the job of a staff writer).