Row colour problem with longtable, multicolumn and makecell

Combination of longtable, makecell and booktabs is not good combination for what you like to achieve. If you will change your MWE to

\documentclass{article}

\usepackage{longtable, makecell, booktabs}
\usepackage[table]{xcolor}
\begin{document}
    \begin{longtable}{@{} m{0.1\linewidth} m{0.8\linewidth} @{}}
        \toprule
    \rowcolor{gray!30}
    \multicolumn{2}{p{0.9\linewidth}}{\makecell{Top line\\Bottom line}}\\  % <---
        \midrule
        \endhead
        a & b   \\
        \bottomrule
    \end{longtable}
\end{document}

than you will get:

Using longtblr of tabularray package may require some learning steps, but with it you can get the following result:

In this case the MWE is:

\documentclass{article}

\usepackage{xcolor}
\usepackage{tabularray}
\UseTblrLibrary{booktabs}

\begin{document}
    \begin{longtblr}[
caption = {Caption},
  label = {longtab:1}
                    ]{colspec = {m{0.1\linewidth} m{0.9\linewidth}},
                      cell{1}{1}  = {c=2}{c, bg=gray!30},
                      hspan   = minimal,
                      rowhead = 1
                      }
        \toprule
{Top line\\Bottom line}
    &       \\
        \midrule
a   &   b   \\
        \bottomrule
    \end{longtblr}
\end{document}

It seems better to replace \makecell with \shortstack inside the merged header cell. The color is set at the cell level, so \rowcolor is redundant. I added \addlinespace to fine-tune the vertical spacing under the header—feel free to remove it if you don’t need it.

\documentclass{article}

\usepackage{array}
\usepackage{booktabs}
\usepackage{longtable}
\usepackage[table]{xcolor}

\begin{document}

\begin{longtable}{@{}m{0.1\linewidth} m{0.88\linewidth}@{}}
\toprule\endhead
\addlinespace[-0.6ex] 
%\rowcolor{gray!30}
\multicolumn{2}{>{\columncolor{gray!30}}c}{\shortstack{Top line\\Bottom line}}\\
\addlinespace[-0.5ex]
\bottomrule
a & b\\

\end{longtable}

\end{document}