i think some are used for emphasis. certain words mean the same, but if you word them differently then they kind of almost have like a different meaning. this is true for translating also, like i know sometimes when i am translating like with my grandma or something, its hard to get the exact meaning, so you try to show the same emphasis on words.
What do you mean words that mean the same thing? Do you mean scientific words vs everyday words? If so, thats because scientific words are heavily based on Latin or Greek origin. As time goes on, words, vocabulary change. So scientists decided to use words of Latin and Greek origin because those words will not change and will stay consistent.
It may seem like words mean the same thing, but often times, they have different meanins that may clarify something you are trying to say. For example: you may thing help and aid mean the same thing, and in some cases they might. But you would probably say "Can I help you" rather than "Can I aid you". Or You might say "They came to their aid" rather than "They came to their help".