Using the font Arial and
\newfontfamily\hebrewfont[Script=Hebrew]{Arial}
\newfontfamily\hebrewfonttt[Script=Hebrew]{Arial}
\newfontfamily\hebrewfontsf[Script=Hebrew]{Arial}
I get the same result.
But with
\setmainfont{Arial}
\setmonofont{Arial}
\setsansfont{Arial}
the result is fine

(I am using TeXstudio, so I removed the LyX specific LaTeX commands. They are not needed with xelatex or lualatex. They will be set by the a4paper of the class. https://tex.stackexchange.com/a/425649/161015 )
\documentclass[a4paper,english,hebrew,numbers=noenddot]{scrartcl}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{fontspec}
\usepackage{fancyhdr}
\pagestyle{fancy}
\setlength{\parindent}{0bp}
\usepackage{color}
\usepackage{pifont}
\usepackage[unicode=true,pdfusetitle,
bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
breaklinks=false,pdfborder={0 0 0},pdfborderstyle={},backref=false,colorlinks=true]
{hyperref}
\hypersetup{
linkcolor=blue}
\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
%\pdfpageheight\paperheight
%\pdfpagewidth\paperwidth
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
%\newfontfamily\hebrewfont[Script=Hebrew]{DavidCLM}
%\newfontfamily\hebrewfonttt[Script=Hebrew]{Miriam Mono CLM}
%\newfontfamily\hebrewfontsf[Script=Hebrew]{Bellefair}
%% IT DOES NOT WORK
%\newfontfamily\hebrewfont[Script=Hebrew]{Arial}
%\newfontfamily\hebrewfonttt[Script=Hebrew]{Arial}
%\newfontfamily\hebrewfontsf[Script=Hebrew]{Arial}
% THIS WORKS OK ! <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
\setmainfont{Arial}
\setmonofont{Arial}
\setsansfont{Arial}
\AtBeginDocument{
\renewcommand\footnoterule{%
\kern -3pt
\hbox to \textwidth{\hfill\vrule height 0.4pt width .4\textwidth}
\kern 2.6pt
}}
% Commands:
\makeatother
\usepackage{polyglossia}
\setdefaultlanguage{hebrew}
\setotherlanguage{english}
\begin{document}
\tableofcontents{}
\part{שלום}
\section{שלום}
\begin{english}
abcd
\end{english}
\end{document}
Using other fonts. In this example the .ttf files in sub-directories under the directory FONTS of the working directory.


% !TeX TS-program = xelatex
\documentclass[a4paper,english,hebrew,numbers=noenddot]{scrartcl}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{fontspec}
\usepackage{fancyhdr}
\pagestyle{fancy}
\setlength{\parindent}{0bp}
\usepackage{color}
\usepackage{pifont}
\usepackage[unicode=true,pdfusetitle,
bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
breaklinks=false,pdfborder={0 0 0},pdfborderstyle={},backref=false,colorlinks=true]
{hyperref}
\hypersetup{
linkcolor=blue}
\usepackage{polyglossia}
\setdefaultlanguage{hebrew}
\setotherlanguage{english}
% using other fonts. .ttf files in subdirectories under the directory FONTS of the working directory <<<<<<<<<<<<<<<<
\setmainfont[
Path =./FONTS/TaameyDavidCLM/,
Ligatures = TeX ,
Script = Hebrew,
Extension=.ttf,
UprightFont=-Medium ,
BoldFont=-Bold,
ItalicFont=-MediumOblique,
BoldItalicFont=-BoldOblique,
Scale=1.0 % Adjust to match Latin font
]{TaameyDavidCLM}
\setmonofont[
Path =./FONTS/MiriamMonoCLM/,
Script = Hebrew,
Extension=.ttf,
UprightFont=-Book,
BoldFont=-Bold,
ItalicFont=-BookOblique,
BoldItalicFont=-BoldOblique,
Scale=1.0 % Adjust to match Latin font
]{MiriamMonoCLM}
\setsansfont[
Path =./FONTS/DejaVuSans/,
Ligatures = TeX ,
Script = Hebrew,
Extension=.ttf,
UprightFont=* ,
BoldFont=-Bold,
ItalicFont=-Oblique,
BoldItalicFont=*-BoldOblique,
Scale=1.0 % Adjust to match Latin font
]{DejaVuSans}
\AtBeginDocument{
\renewcommand\footnoterule{%
\kern -3pt
\hbox to \textwidth{\hfill\vrule height 0.4pt width .4\textwidth}
\kern 2.6pt
}}
\begin{document}
\tableofcontents
\part{שלום}
\section{שלום}
\begin{english}
abcd
\end{english}
\section{בראשית}
\textbf{בְּרֵאשִׁ֖ית}
\textit{יְהִ֣י א֑וֹר}
\bigskip
\texttt{ \textbf{וַיַּ֧רְא אֱלֹהִ֛ים אֶת־הָא֖וֹר כִּי־ט֑וֹב וַיַּבְדֵּ֣ל אֱלֹהִ֔ים בֵּ֥ין} הָא֖וֹר וּבֵ֥ין הַחֹֽשֶׁךְ׃ }
\section{מבוא}
זוהי עובדה מבוססת שדעתו של הקורא תהיה מוסחת עלידי טקטס קריא כאשר הוא יביט בפריסתו.
\end{document}
\tracinglostchars=3, to make it an error when you try to use characters the font does not have? – Davislor Jun 30 '22 at 11:38