\setmainstyle命令的问题是它将在帧内使用，因此是无效的。
为了避免这个问题，你可以使用与https://tex.stackexchange.com/questions/173201/beamer-template-with-different-style-options-for-frames相同的策略来创建一个框架选项，它将改变背景。
不幸的是，rmarkdown简单地忽略了用户创建的帧选项，只传递了一个预定义选项的小列表。为了欺骗rmarkdown，可以重新使用beamer通常不使用的帧选项，standout帧选项（它只被大都会主题使用）

---
output: 
  beamer_presentation:
    keep_tex: true
header-includes: |
  \usepackage{etoolbox}

  \defbeamertemplate{background canvas}{mydefault}{%
    \includegraphics[width=\paperwidth,height=\paperheight]{example-image-duck}
  }
  \defbeamertemplate{background canvas}{standout}{%
    \includegraphics[width=\paperwidth,height=\paperheight,page=2]{example-image-duck}
  }

  \BeforeBeginEnvironment{frame}{%
    \setbeamertemplate{background canvas}[mydefault]%
  }

  \makeatletter
  \define@key{beamerframe}{standout}[true]{%
    \setbeamertemplate{background canvas}[standout]%
  }
  \makeatother

---

# frametitle 

test

# frametitle with different background {.standout}

test

# frametitle

test

或者如果要更改以下所有帧的背景：

\usepackage{etoolbox}

\defbeamertemplate{background canvas}{mydefault}{%
  \includegraphics[height=\paperheight,page=2]{example-image-duck}
}
\defbeamertemplate{background canvas}{standout}{%
  \includegraphics[height=\paperheight]{example-image-duck}
}

\setbeamertemplate{background canvas}[mydefault]%

\makeatletter
\define@key{beamerframe}{standout}[true]{%
  \setbeamertemplate{background canvas}[standout]%
}
\makeatother

更新：

Pandoc现在允许任意帧选项（https://github.com/jgm/pandoc/commit/7fbce82f2f7b69e88b23cf138ea6cd3a86786b91）

---
output: 
  beamer_presentation:
header-includes: |

  \defbeamertemplate{background canvas}{mydefault}{}
  \defbeamertemplate{background canvas}{special}{%
    \includegraphics[width=\paperwidth,height=\paperheight]{example-image-duck}
  }

  \BeforeBeginEnvironment{frame}{%
    \setbeamertemplate{background canvas}[mydefault]%
  }

  \makeatletter
  \define@key{beamerframe}{special}[true]{%
    \setbeamertemplate{background canvas}[special]%
  }
  \makeatother

---

# frametitle 

test

# Heading {frameoptions="special"}

test

# frametitle 

test