You can work with bookmarksdepth
\documentclass[toc=flat,numbers=noenddot]{scrartcl}
\usepackage[english]{babel}
\usepackage{blindtext}
\usepackage{hyperref}
\makeatletter
\newcommand*{\maintoc}{%
\begingroup
\@fileswfalse
\renewcommand*{\appendixattoc}{%
\value{tocdepth}=-10000%
}%
\tableofcontents%
\endgroup
}
\newcommand*{\appendixtoc}{
\begingroup
\edef\@alltocdepth{\the\value{tocdepth}}%
\setcounter{tocdepth}{-10000}%
\renewcommand*{\contentsname}{%
List of Appendices}%
\renewcommand*{\appendixattoc}{%
\setcounter{tocdepth}{\@alltocdepth}%
}%
\tableofcontents%
\setcounter{tocdepth}{\@alltocdepth}%
\endgroup
}
\newcommand*{\appendixattoc}{}%
\g@addto@macro\appendix{%
\clearpage%
\phantomsection%
\addcontentsline{toc}{section}{\appendixname}%
\addtocontents{toc}{\protect\appendixattoc}%
\renewcommand*{\thesection}{Appendix~\Alph{section}}%
}
\makeatother
\begin{document}
\maintoc
\blinddocument
\hypersetup{bookmarksdepth=-1}
\appendix
\pdfbookmark[-1]{Appendix}{appendixentry}
\appendixtoc
\hypersetup{bookmarksdepth=4}
\blinddocument
\end{document}

EDIT:
You can also modify the interna of the level -- here I changed them in the following way:
\g@addto@macro\appendix{%
\clearpage%
\phantomsection%
\addcontentsline{toc}{section}{\appendixname}%
\addtocontents{toc}{\protect\appendixattoc}%
\renewcommand*{\thesection}{Appendix~\Alph{section}}%
\def\toclevel@chapter{1}%0
\def\toclevel@section{2}%1
\def\toclevel@subsection{3}%2
\def\toclevel@subsubsection{4}%
\def\toclevel@paragraph{5}%
\def\toclevel@subparagraph{6}%
\def\toclevel@figure{7}%
\def\toclevel@table{8}%
}
The result is the same:
\documentclass[toc=flat,numbers=noenddot]{scrartcl}
\usepackage[english]{babel}
\usepackage{blindtext}
\usepackage{hyperref}
\usepackage{bookmark}
\makeatletter
\newcommand*{\maintoc}{%
\begingroup
\@fileswfalse
\renewcommand*{\appendixattoc}{%
\value{tocdepth}=-10000%
}%
\tableofcontents%
\endgroup
}
\newcommand*{\appendixtoc}{
\begingroup
\edef\@alltocdepth{\the\value{tocdepth}}%
\setcounter{tocdepth}{-10000}%
\renewcommand*{\contentsname}{%
List of Appendices}%
\renewcommand*{\appendixattoc}{%
\setcounter{tocdepth}{\@alltocdepth}%
}%
\tableofcontents%
\setcounter{tocdepth}{\@alltocdepth}%
\endgroup
}
\newcommand*{\appendixattoc}{}%
\g@addto@macro\appendix{%
\clearpage%
\phantomsection%
\addcontentsline{toc}{section}{\appendixname}%
\addtocontents{toc}{\protect\appendixattoc}%
\renewcommand*{\thesection}{Appendix~\Alph{section}}%
\def\toclevel@chapter{1}
\def\toclevel@section{2}
\def\toclevel@subsection{3}
\def\toclevel@subsubsection{4}
\def\toclevel@paragraph{5}
\def\toclevel@subparagraph{6}
\def\toclevel@figure{7}
\def\toclevel@table{8}
}
\makeatother
\begin{document}
\maintoc
\blinddocument
\appendix
\appendixtoc
\blinddocument
\end{document}
EDIT: Changed the order of \appendix and \pdfbookmark