Headers are tricky. Ive worked with many engine builders building headers for show cars and all out race cars for a while now.
The manufactures are building exhaust system with many limitations that dont apply to "us" (performance oriented enthusiasts) that is why many aftermarket companies can claim better performance but you must also ask yourself where in the rpm band are they better?
To answer your 2nd question yes the must be built to take in consideration all the things that you mentioned. BUT there are some generic changes that can be made to make the stock herder design "generically" better.
To get the best performance a custom set should be built. But it in not typically in the budget of the build unless it is a race car or no one makes headers for the application that someone has put together, at least this is what i have found in approx a decade of building headers
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