5. hitting "C-return" will randomize font once, which might be useful for you find debug,

Expected behavior:

the fonts are rendered consistently without extra spacing,

Observed behavior:

the fonts are rendered with extra spacing randomly,

Related information:

I previously reported this bug here: https://github.com/mickeynp/ligature.el/issues/56.

In GNU Emacs 29.4 (build 1, x86_64-redhat-linux-gnu, GTK+ Version

3.24.42, cairo version 1.18.0) of 2024-07-16 built on
27527c2e06f843c0962737354e0b3cf7
System Description: Fedora Linux 40 (Sway)

Configured using:
'configure --build=x86_64-redhat-linux-gnu
--host=x86_64-redhat-linux-gnu --program-prefix=
--disable-dependency-tracking --prefix=/usr --exec-prefix=/usr
--bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc
--datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64
--libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run
--sharedstatedir=/var/lib --mandir=/usr/share/man
--infodir=/usr/share/info --with-cairo --with-dbus --with-gif
--with-gpm=no --with-harfbuzz --with-jpeg --with-json --with-modules
--with-native-compilation=aot --with-pgtk --with-png --with-rsvg
--with-sqlite3 --with-tiff --with-tree-sitter --with-webp --with-xpm
--with-xwidgets build_alias=x86_64-redhat-linux-gnu
host_alias=x86_64-redhat-linux-gnu CC=gcc 'CFLAGS=-DMAIL_USE_LOCKF -O2
-flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches
-pipe -Wall -Werror=format-security
-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS
-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong
-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64
-mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection
-fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
LDFLAGS=-Wl,-z,relro
PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig CXX=g++
'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g
-grecord-gcc-switches -pipe -Wall -Werror=format-security
-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS
-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong
-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64
-mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection
-fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ''

Configured features:
ACL CAIRO DBUS FREETYPE GIF GLIB GMP GNUTLS GSETTINGS HARFBUZZ JPEG JSON
LIBOTF LIBSELINUX LIBSYSTEMD LIBXML2 MODULES NATIVE_COMP NOTIFY INOTIFY
PDUMPER PGTK PNG RSVG SECCOMP SOUND SQLITE3 THREADS TIFF
TOOLKIT_SCROLL_BARS TREE_SITTER WEBP XIM XWIDGETS GTK3 ZLIB

Important settings:
value of $LANG: en_US.UTF-8
locale-coding-system: utf-8-unix

Major mode: ELisp/l

Minor modes in effect:
global-ligature-mode: t
ligature-mode: t
tooltip-mode: t
global-eldoc-mode: t
eldoc-mode: t
show-paren-mode: t
electric-indent-mode: t
mouse-wheel-mode: t
tool-bar-mode: t
menu-bar-mode: t
file-name-shadow-mode: t
global-font-lock-mode: t
font-lock-mode: t
blink-cursor-mode: t
line-number-mode: t
indent-tabs-mode: t
transient-mark-mode: t
auto-composition-mode: t
auto-encryption-mode: t
auto-compression-mode: t

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message yank-media puny dired
dired-loaddefs rfc822 mml mml-sec epa derived epg rfc6068 epg-config
gnus-util text-property-search time-date mm-decode mm-bodies mm-encode
mail-parse rfc2231 mailabbrev gmm-utils mailheader sendmail rfc2047
rfc2045 ietf-drums mm-util mail-prsvr mail-utils comp comp-cstr warnings
icons rx ligature cl-extra help-mode use-package-core ligature-autoloads
package browse-url url url-proxy url-privacy url-expand url-methods
url-history url-cookie generate-lisp-file url-domsuf url-util mailcap
url-handlers url-parse auth-source cl-seq eieio eieio-core cl-macs
password-cache json subr-x map byte-opt gv bytecomp byte-compile
url-vars cl-loaddefs cl-lib rmc iso-transl tooltip cconv eldoc paren
electric uniquify ediff-hook vc-hooks lisp-float-type elisp-mode mwheel
term/pgtk-win pgtk-win term/common-win pgtk-dnd tool-bar dnd fontset
image regexp-opt fringe tabulated-list replace newcomment text-mode
lisp-mode prog-mode register page tab-bar menu-bar rfn-eshadow isearch
easymenu timer select scroll-bar mouse jit-lock font-lock syntax
font-core term/tty-colors frame minibuffer nadvice seq simple cl-generic
indonesian philippine cham georgian utf-8-lang misc-lang vietnamese
tibetan thai tai-viet lao korean japanese eucjp-ms cp51932 hebrew greek
romanian slovak czech european ethiopic indian cyrillic chinese
composite emoji-zwj charscript charprop case-table epa-hook
jka-cmpr-hook help abbrev obarray oclosure cl-preloaded button loaddefs
theme-loaddefs faces cus-face macroexp files window text-properties
overlay sha1 md5 base64 format env code-pages mule custom widget keymap
hashtable-print-readable backquote threads xwidget-internal dbusbind
inotify dynamic-setting system-font-setting font-render-setting cairo
gtk pgtk multi-tty make-network-process native-compile emacs)

Memory information:
((conses 16 108675 14724)
(symbols 48 8830 0)
(strings 32 27784 2658)
(string-bytes 1 906120)
(vectors 16 22224)
(vector-slots 8 441624 17378)
(floats 8 45 30)
(intervals 56 736 1)
(buffers 984 12))