Use parskip package instead of setting \parskip ourselves.

sphinx/texinputs/sphinx.sty

@@ -26,6 +26,8 @@
 \makesavenoteenv{tabulary}
 % For floating figures in the text.
 \RequirePackage{wrapfig}
+% Separate paragraphs by space by default.
+\RequirePackage{parskip}
 
 % Redefine these colors to your liking in the preamble.
 \definecolor{TitleColor}{rgb}{0.126,0.263,0.361}
@@ -89,8 +91,6 @@
 % Style parameters and macros used by most documents here
 \raggedbottom
 \sloppy
-\parindent = 0mm
-\parskip = 2mm
 \hbadness = 5000                % don't print trivial gripes
 
 \pagestyle{empty}               % start this way; change for