Weird vertical spacing with custom tcolorbox and tabular environment

I am not sure why these boxes are not aligning but I would do this differently and use a sidebyside tcolorbox. If you define:

newtcolorbox{CODE}{
    sidebyside,
    sidebyside align=top,
    colback=light-gray,
    colframe=white,
    bicolor,
    colbacklower=white,
    righthand width=2.5in
}
newcommandCode[2]{begin{CODE}#1tcblower#2end{CODE}}

Then you can replace your method section with

    begin{methodt}{Rectangles}
      Code{rect(x, y, width, height)}{A rectangle whose top-left corner is at (x, y); Pen automatically moved}
      Code{fillRect(x, y, width, height)}{A solid rectangle}
      Code{strokeRect(x, y, width, height)}{An outline rectangle}
      Code{clearRect(x, y, width, height)}{Clear a portion or all of a rectangle}
    end{methodt}

(I have removed the tabular environment from the methodt environment) to produce:

Here is the full code:

documentclass{article}

usepackage{tabularx}  % Allows easy wrapping of text in tables
usepackage{setspace}  % Allows setting line spacing throughout document
usepackage{listings}  % Used for code sections
usepackage{color}     % Used to define colors
usepackage[a4paper, total={6in, 8in}]{geometry}  % Used to set page dimensions
geometry{             % Setting margins
    top = 1in,
    bottom = 1in
}
usepackage{hyperref}  % Allows blue styling of links and clickable table of contents
hypersetup{
    colorlinks,
    linkcolor = blue
}

% Following allows inline code
usepackage{tcolorbox}
tcbuselibrary{skins}
definecolor{dark-gray}{gray}{0.85}
definecolor{light-gray}{gray}{.95}
%newtcolorbox[〈init options〉]{〈name〉}[〈number〉][〈default〉]{〈options〉}

newtcolorbox{CODE}{
    sidebyside,
    sidebyside align=top,
    colback=light-gray,
    colframe=white,
    bicolor,
    colbacklower=white,
    righthand width=2.5in
}
newcommandCode[2]{begin{CODE}#1tcblower#2end{CODE}}

newtcolorbox{exbox} {
    colback=white,
    colframe=white
}
newcommand{ex}[1] {%
    begin{exbox}
        {#1}
    end{exbox}%
'}


%renewcommand*arraystretch{1.085}  % Setting vertical spacing in tables

newcommand{secspace}{vspace{ .25in }}  % Separator between sections
newcommand{secline}{vspace{ 6pt } hrule width 2in vspace{ 6pt }}  % Horizontal line between section title and content
newenvironment{methodt}[1]  % Table for use with methods. Left side is method, right side is description
    {%
        subsection{ #1 }
        secline
    }
    {%
        secspace
    }

% Defining colors for use in code segments
definecolor{lightgray}{rgb}{.95,.95,.95}
definecolor{darkgray}{rgb}{.4,.4,.4}
definecolor{purple}{rgb}{0.65, 0.12, 0.82}

% Defining the JavaScript language
lstdefinelanguage{JavaScript}{
    keywords={typeof, new, true, false, catch, function, return, null, catch, switch, var, if, in, while, do, else, case, break},
    keywordstyle=color{blue}bfseries,
    ndkeywords={class, export, boolean, throw, implements, import, this},
    ndkeywordstyle=color{darkgray}bfseries,
    identifierstyle=color{black},
    sensitive=false,
    comment=[l]{//},
    morecomment=[s]{/*}{*/},
    commentstyle=color{purple}ttfamily,
    stringstyle=color{red}ttfamily,
    morestring=[b]',
    morestring=[b]"
}

% Setting properties of code blocks
lstset{
    language=JavaScript,
    backgroundcolor=color{lightgray},
    extendedchars=true,
    basicstyle=footnotesizettfamily,
    showstringspaces=false,
    showspaces=false,
    numbers=none,
    numberstyle=footnotesize,
    numbersep=9pt,
    tabsize=2,
    breaklines=true,
    showtabs=false,
    captionpos=b
}

begin{document}
    setstretch{1.1}  % Set line spacing across document

    begin{titlepage}
        vspace*{stretch{1.0}}
        begin{center}
            Largetextbf{Web Canvas API Reference --- Lite}
            largetextbf{ Alex Eastman }
        end{center}
        vspace*{stretch{2.0}}
    end{titlepage}
    clearpage

    begin{flushleft}
        tableofcontents
        clearpage

        section{Methods} label{methods}

        % Rectangles
        begin{methodt}{Rectangles}
          Code{rect(x, y, width, height)}{A rectangle whose top-left corner is at (x, y); Pen automatically moved}
          Code{fillRect(x, y, width, height)}{A solid rectangle}
          Code{strokeRect(x, y, width, height)}{An outline rectangle}
          Code{clearRect(x, y, width, height)}{Clear a portion or all of a rectangle}
        end{methodt}

end{flushleft}

end{document}

Btw, I would also the xcolor package package, instead of color...although I can not point to anywhere where this would make a difference:)