I would say a few things would play into a sleeper look for a engine bay, but mostly color. Like satin or flat black intercooler piping and intercooler, black rubber boots for the intercooler piping as well. When you put a fuel pressure regulator on, you could look for one that is already black or have it powder coated so. If you run stainless braided lines, get them in black or have rubber hoses made with the correct fittings on the ends.
Next I would say a heat shield over the exhaust housing on the turbo will help with temperature control and would look more factory.
No matter how hard you try, It won’t be that hard to spot aftermarket parts but you can do your best to conceal them. Good luck!