# With nodes (expected output)

\documentclass[pstricks,border=12pt]{standalone}
\usepackage{pst-node}
\begin{document}
\begin{pspicture}[showgrid=t,dimen=m](-2,0)(2,4)
\pnode(0,3){A}
\qdisk(A){3pt}
\qdisk(B){3pt}
\qdisk(C){3pt}
\pscircle(A){1}
\psarc[linecolor=red,origin={A}](A){1}{(B)}{(C)}
\end{pspicture}
\end{document}


# With literals

\documentclass[pstricks,border=12pt]{standalone}
\usepackage{pst-node}
\begin{document}
\begin{pspicture}[showgrid=t,dimen=m](-2,0)(2,7)
\qdisk(0,3){3pt}
\pscircle(0,3){1}
\end{pspicture}
\end{document}


# Question

How to fix the second one such that its output is similar to the first one?

In your second example the coordinates seems to be calculated relative to (0,3), so you don't have to add 3. Nodes you set before are fixed and not relative.

\documentclass[pstricks,border=12pt]{standalone}
\usepackage{pst-node}
\begin{document}
\makeatletter
\begin{pspicture}[showgrid=t,dimen=m](-2,0)(2,7)
\qdisk(0,3){3pt}