\listofschemes from chemmacros not working with KOMA script commands

Package chemmacros checkes at begin document if a KOMA-Script class is used or if package tocbasic is loaded manually (with another class). Then it defines the new list for the schemes using \DeclareNewTOC. So you have to defer the change of indent and numwidth for TOC entries scheme using \AtBeginDocument, too.

Use

\AtBeginDocument{\DeclareTOCStyleEntry[indent=0em,numwidth=2.3em]{default}{scheme}}

to ensure that scheme is already defined by chemmacros when you change its indent and numwidth. Note that you do the same for your redefinition of \thescheme.

Example:

\documentclass[fontsize=10pt,
  twoside,
  paper=b5,
  pagesize=auto,
  numbers=noenddot,
  toc=bibliography,
  listof=totoc,
  open=right,
  %singlespacing=true,% not used in the example
  chapterprefix=true,
  appendixprefix=true
  ]{scrreprt}
%
\usepackage{scrhack}% Patches for KOMA-script.
\usepackage[american]{babel}
%
\usepackage{blindtext}% only for dummy text
%
%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{float}
\usepackage{chemmacros}
\usechemmodule{mechanisms,%
  redox,%
  spectroscopy,%
  units,%
  scheme}
 \AtBeginDocument{%
  \renewcommand{\thescheme}{\arabic{chapter}.\arabic{scheme}}%
  \DeclareTOCStyleEntry[indent=0em,numwidth=2.3em]{default}{scheme}% <- moved
}
%
\DeclareTOCStyleEntry[indent=0em,numwidth=2.3em]{default}{figure}
%
\begin{document}
\chapter{A chapter}
\blindtext
\begin{figure}[H]
\caption{blabla}
  \label{fig:1}
\end{figure}
\begin{figure}[H]
\caption{blabla}
  \label{fig:2}
\end{figure}
\begin{figure}[H]
\caption{blabla}
  \label{fig:3}
\end{figure}
\begin{figure}[H]
\caption{blabla}
  \label{fig:4}
\end{figure}
\blindtext
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:1}
\end{scheme}
\chapter{Another chapter}
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:2}
\end{scheme}
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:3}
\end{scheme}
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:4}
\end{scheme}
%
\blindtext
\listoffigures
\listofschemes
\end{document}

Result:

Well, it seems that chemmacros (2017) is based on an meanwhile changed version of tocbasic of KOMA-Script.

You should contact the maintainer of chemmacros and write an bug report (if you want you can use this question/answer as example).

A quick workaround can be to simply add the following lines in your preamble (please see important code changes marked with <=========):

\DeclareNewTOC[% <======================================================
  type=scheme,%
  types=schemes,%
  float,% Gleitumgebungen sollen definiert werden.
  floattype=4,%
  name=Scheme,%
  listname={List of schemes}%
]{scheme}
\setuptoc{scheme}{chapteratlist} % <==================================== 

So with the complete MWE

\documentclass[%
  fontsize=10pt,
  twoside,
  paper=b5,
  pagesize=auto,
  numbers=noenddot,                % Removes ending point after heading- and caption numbers.
  toc=bibliography,                % Includes bibliography into ToC but without numbering it.
  listof=totoc,                    % Includes all lists (figures, etc.) into ToC but without numbering.
  open=right,                      % Start new chapters on a right page (doublepage layout).
  singlespacing=true,              % KOMA-script. p 450ff. setspace only in textbody.
  chapterprefix=true,
  appendixprefix=true
]{scrreprt}                                  
%
\usepackage{scrhack}                             % Patches for KOMA-script.
\usepackage[american]{babel}
\usepackage{amsmath}                                 
%\usepackage[final,tracking=true]{microtype} % <================================                                    
\usepackage{fontspec}                            
\defaultfontfeatures{
 Ligatures = TeX ,                           
     RawFeature={+calt} ,                        
 SmallCapsFeatures={Letters=SmallCaps}
 }                
\usepackage[math-style=ISO,
                    bold-style=ISO]{unicode-math}                                   
\usepackage{libertinus}                                                      
%
\usepackage{blindtext}
%
%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{float}                                                                      
\usepackage[compatibility=newest]{chemmacros} % <=======================
\usechemmodule{%
  mechanisms,%                      
  redox,%                           
  spectroscopy,%
  units,%
  scheme
}
\AtBeginDocument{\renewcommand{\thescheme}{\arabic{chapter}.\arabic{scheme}}}
%%%%%%%%%%%%%%%%%%%%%%%%
%
\DeclareTOCStyleEntry[indent=0em,numwidth=2.3em]{dottedtocline}{figure}
\DeclareNewTOC[% <======================================================
  type=scheme,%
  types=schemes,%
  float,% Gleitumgebungen sollen definiert werden.
  floattype=4,%
  name=Scheme,%
  listname={List of schemes}%
]{scheme}
\setuptoc{scheme}{chapteratlist} % <====================================
\DeclareTOCStyleEntry[indent=0em,numwidth=2.3em]{dottedtocline}{scheme}
%
%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
%
\blindtext
%
\begin{figure}[H]
\caption{blabla}
  \label{fig:1}
\end{figure}
\begin{figure}[H]
\caption{blabla}
  \label{fig:2}
\end{figure}
\begin{figure}[H]
\caption{blabla}
  \label{fig:3}
\end{figure}
\begin{figure}[H]
\caption{blabla}
  \label{fig:4}
\end{figure}
%
\blindtext
%
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:1}
\end{scheme}
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:2}
\end{scheme}
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:3}
\end{scheme}
\begin{scheme}[H]
\caption{blabla}
  \label{scheme:4}
\end{scheme}
%
\blindtext
%
\listoffigures
\listofschemes
%
\end{document}

I get the following resulting scheme list:

Please see: That is only a workaround, the maintainer should be asked to correct the package!