It means that two things or situations may not be exactly the same, but they are the same in everything that is important.
"Reading an eBook on a screen, and turning the pages of a book printed on paper, are very different in technology, but the reading experience is the same in all essentials."
"Along with changes in uniforms, stadiums, and equipment, the rules of baseball have evolved over the years. Nevertheless, baseball today is the same game that Babe Ruth played, in all essentials."
"In choosing between Android and iOS smartphones, people express strong preferences. However, the reality is that they are the same in all essentials."