That's "meta data" compiler information. It's no TeX and no LaTeX instruction. From LaTeX's point of view, it's just a comment, since it starts with %. There are LaTeX editors that support compiler information in documents, provided within comments, such as here.
Here, it's information for the TeXshop editor (TS) on Mac PCs or Macbooks. The first line means, that the pdfLaTeX compiler shall be used, and the second lines determines that utf8 unicode should be used, for the TeX compiler.
Other editors (and compilers) would ignore those lines. And it's pretty default anyway.
Sometimes a template author wants to define the way the template is used/compiled, as here. Like preventing accidental use of XeLaTeX or LuaLaTeX or a non-standard encoding. These two lines say something like "use default common settings".
Johannes is right! Just by the way, some people use more %%%%% signs just to mark comments better visible or to highlight information in the code or "borders", such as
\frontmatter
some code
some text
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% here the front matter ends %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\mainmatter
\section{One}
After a single % that starts a comment, it doesn't matter. And some LaTeX editors highlight comments in a different way.