makeatletter
documentclass[draft]{article}

usepackage{marginnote}
usepackage{ifdraft}
usepackage{lipsum}

newifif@use@leavevmode@hack

newcounter{commentnote}
newcommand{commentnote}[2][0pt]{%
  newifif@cnmark
  unlessifvmode
    unskip
    @cnmarktrue
    stepcounter{commentnote}%
  else
    if@use@leavevmode@hack
      leavevmode
    fi
  fi
  ifdraft{%
    if@cnmarktextsuperscript{thecommentnote}fi
    marginnote{if@cnmarktextsuperscript{thecommentnote},fi#2}[#1]%
  }{}%
}

begin{document}

section{Without textbackslash leavevmode}

sloppy

commentnote{Note (1)}
This text should not be indented.

The verb|unlessifvmodeunskip|
was introduced to allow
  commentnote{Note(2)}
typesetting notes on separate lines without adding
% characters at the end of each preceding line,
and in order to use verb|commentnote|
in vertical mode to create unmarked comments.

commentnote{Note(3)}
commentnote[baselineskip]{Note (4)}
commentnote[2baselineskip]{Note (5)}

It is acceptable to use multiple notes before a paragraph.
Inserting verb|leavevmode| would cause spurious numbering.


section{With textbackslash leavevmode}
@use@leavevmode@hacktrue

commentnote{Foo}%
Using verb|leavevmode| leads to correct indentation,
but then requires manually removing newlines between
verb|commentnote| and paragraphs, and adding %
characters at the end of each invocation.

commentnote{Note(3)}%
commentnote[baselineskip]{Note (4)}%
commentnote[2baselineskip]{Note (5)}%
Furthermore, it leads to spurious numbering of out-of-paragraph notes.

end{document}