You said, "If some combinations are feasible, but based on literature it will not be as effective, should I make it a disallowed combination?" That question demonstrates that you have a 'testing' mindset, not an 'experimenting' mindset. A test provides an answer. An experiment provides a model (lots of answers). It is not a matter of 'right or wrong.' It is a matter of being clear about your purpose. Either mindset might be right depending on your goal. You can keep testing until you find what you want ('trial and error'), or you can run a designed experiment, fit a model, and use the model to explore the space to find what you want.
You add constraints when some conditions in the regular design space are impossible, dangerous, or would change the phenomenon under study. Otherwise, you want to observed the entire design space as efficiently and effectively as possible. Because you want to estimate the model parameters.
A good experiment will illicit both good and bad responses. That way, you have a realistic model that can predict the entire range of outcomes.
You said, "Out of seven factors, two factors (level 0 and 1) are said to work better together rather than alone." This observation indicates that an interaction effect is important in the response. Eliminating the combinations of (0,1) and (1,0) will make it impossible to model that interaction. The data will be devoid of the necessary information without those combinations.