1 Why is it generally presumed that transsexual gender identities and sex embodiments are inherently less natural and less legitimate than those of non transsexual people?

Most of the reasons are social ones, though there is also a biological one. Socially, religion still plays a major role in how the world operates. Some of the largest religions teach that things that go against the imagined norms, such as transsexual, intersexed, homosexual, etc. people are a sin against nature and/or God. The religions themselves aren't necessarily the problem, but the varied interpretations and resulting actions by the followers are.

Next would be the the biological one. Instinctually, humans are afraid of things that are vastly different from what they are normally surrounded by. Humans are also afraid of things that they do not understand. This acts as a very basic, although effective, survival mechanism. Keep to the familiar, avoid the unfamiliar, and you are more likely to live longer. Unfortunately, that basic instinct only works well in the wild. In a social setting, it can be ineffective or downright harmful to your ability to grow and function with other humans. Most people do not know transsexual people. This lack of knowledge of what a transsexual person is like leads to fear. Wild speculation, stereotypes, and outright fabrications of the truth fuel this fear.

In the same vein, those in power generally want to keep in power. They fear losing their power or status. They will do whatever they can to keep their position safe. This includes keeping those that are different from them trapped on a lower rung of the social ladder. It happened, and continues to happen, in the United States with non-white people and women, among others. Other countries have the same problem, though the people persecuted differ from country to country.

Ignorance is the biggest factor. Those in power who know the truth (or don't, as the case usually is) will use the ignorance of the masses as their tools to keep a group down. Education and personal interactions with the people who are misunderstood is generally one of the solutions to all of the reasons why people other than those in power are persecuted, this particular example being no different.