Turn on a multi-functional pressure cooker (such as Instant Pot) and select Saute function. Add bacon and brown, 5 to 7 minutes. Add garlic and cook and stir for 30 seconds. Add onion, followed by celery and carrot. Cook and stir for 1 to 2 minutes. Turn off Saute function.
Layer potatoes, then corn, on top of vegetable mixture. Pour in vegetable broth. Lay haddock on top, followed by shrimp and scallops.
Close and lock the lid. Select high pressure according to manufacturer's instructions; set timer for 5 minutes. Allow 10 to 15 minutes for pressure to build.
Release pressure using the natural-release method according to manufacturer's instructions, for 10 minutes. Release remaining pressure carefully using the quick-release method according to manufacturer's instructions, about 5 minutes. Unlock and remove the lid.
Turn the Saute feature on and stir to break up the fish. Add thyme, red pepper flakes, and ground pepper. Mix cornstarch and water together in a measuring cup; stir into chowder and cook until thickened. Stir in milk and serve.