Bad horizontal alignment

\documentclass{article}
\usepackage{amsmath}
\usepackage{mathtools}
\usepackage{lipsum}

\begin{document}\pagestyle{empty}

\lipsum[1]

\noindent Vertical numbering:

\noindent\begin{minipage}{.4\textwidth}
  \begin{align}
    x&=1 \\
    y&=1
  \end{align}
\end{minipage}% <-- % symbol necessary
\begin{minipage}{.6\textwidth}
  \begin{align}
    z&=1\\
    w&=1
  \end{align}
\end{minipage}

\bigskip

\noindent Horizontal numbering:

\noindent\begin{minipage}{0.4\textwidth}
\begin{equation}
x^2 + y = \mathrlap{z + 4}\phantom{z + 4 + y^2 - p} \\
\end{equation}
\end{minipage}
\begin{minipage}{0.6\textwidth}
\begin{equation}
\phantom{x^2 + y^3 - 17}\mathllap{x^2} = z + 4 + q \\
\end{equation}
\end{minipage}\\[-2ex]
\begin{minipage}{0.4\textwidth}
\begin{equation}
\phantom{x^2 + y}\mathllap{x^2} = z + 4 + y^2 - p \\
\end{equation}
\end{minipage}
\begin{minipage}{0.6\textwidth}
\begin{equation}
x^2 + y^3 - 17 = \mathrlap{z}\phantom{z + 4 + q} \\
\end{equation}
\end{minipage}

\vspace{\baselineskip}

\lipsum[2]

\end{document}