In a large stockpot, cook your linguini pasta according to package instructions (9 to 11 minutes). When pasta is done cooking, reserve ½ cup of the starchy pasta water in a separate bowl to be used for later. Drain the remaining liquid. Set aside.
While your pasta is cooking, in a large skillet on medium-high heat saute your butter, onions, everything bagel seasoning, salt, and pepper. Saute the onions for 2 to 3 minutes or until they are soft and translucent.
Add the flour to the onions and cook for another 1 to 2 minutes, until you no longer see raw flour.
Whisk the reserved pasta water into the flour mixture, making sure you do not have any lumps remaining.
Add the cream cheese to the flour and onion mixture. Stir the cream cheese around so that it melts into the flour mixture and is smooth.
Slowly add the milk to the cream cheese mixture. Allow this sauce to cook and thicken for 3 to 5 minutes. Make sure to whisk constantly to avoid any lumps from forming.
Add the grated pecorino-romano cheese to the sauce and stir to combine.
Add the cooked pasta to the sauce and toss it to coat it entirely in the sauce.
You can garnish the Everything Bagel Pasta with the additional everything bagel seasoning and chopped fresh parsley if desired.