Is it permissible to use a website code that states "All rights reserved" on another website, with modifications, knowing that creating a similar code would lead to the same result, and that the code resembles a method of making things?

The phrase "All rights reserved" means the owner of the website has the right to financially and intellectually benefit from its content. It is not permissible to infringe upon this right except with their permission. There is a difference between infringing upon their right to use their proprietary code by changing or deleting it, and creating something similar to their website or code through agreement and convergence of ideas. There is no harm in the latter.