Rotating polar contour plot messes with alignment of plot and axis

For your convenience I added a style, rotate polar axis, that does the rotation and fixes the ticks. For the sake of reproducibility I refrain from using huge data files.

\documentclass[tikz,border=3mm]{standalone}
\usepackage{pgfplots}
\usepgfplotslibrary{polar}
\pgfplotsset{compat=1.16}
\pgfplotsset{rotate polar axis/.style={rotate=#1,xticklabel
style={anchor=\tick+#1+180}}}
\begin{document}
\foreach \X in {0,90,180,270}
{\begin{tikzpicture}
\begin{polaraxis}[rotate polar axis=\X,
width=4in,
height=4in,
tickwidth=0,
xtick distance = 45,
separate axis lines,
y axis line style= { draw opacity=0 },
yticklabels = {},
ymin=0, ymax=1,
axis on top=true, 
] 

    \addplot coordinates {
        (0,1) (90,1/2) (180,1/3) (270,1/4)
    };  
\end{polaraxis}
\node at (current axis.north) [above=1em]{\texttt{rotate polar axis=\X}};
\end{tikzpicture}}
\end{document}