Turn the Instant Pot to sauté. Heat 1 tablespoon of olive oil and add the scallops. Cook for 2 minutes, turning once, then remove and set aside.
Add 1 tablespoon olive oil. Add the finely chopped onions and cook until translucent, about 2-3 minutes.
In a medium bowl, mix both types of tomatoes (do not drain), water, remaining olive oil, balsamic vinegar, garlic, basil, oregano, salt, pepper, and red pepper flakes.
Ladle some tomato mixture into the Instant Pot to cover the bottom.
Break the linguine in half and place on top of the sauce. Pour in the rest of the sauce to cover the linguine well.
Seal the lid and cook on high pressure for 6 minutes. Do a quick release. Open the lid and stir everything together.
Add the shrimp and mussels straight into the pasta. Close the lid and set the Instant Pot to high pressure for 1 more minute. Perform a quick release.
Add the cooked scallops to the mixture. Let stand for 3–5 minutes. The sauce will thicken a bit upon standing.