To answer your first question, yes it is true and it is also true for compiled op-code. Yes you can make your code faster by avoiding function calls except in extreme cases where your code grows too large because of code duplication.
You should do what you like "I like to write well-organized, human-readable code with methods wherever a code block would be repeated."
If your going to commit this horrible atrocity of removing all function calls at least use a profiler and only do it to the 10% of your code that matters.
