In my experience, customizing read-minibuffer-restore-windows to nil
works mostly fine, thanks for the option. The only problem I've
personally encountered is in the following case:

emacs -q:

(setq read-minibuffer-restore-windows nil)
M-x, to open a minibuffer
C-h b, to display a help buffer from this minibuffer
C-g, to quit the minibuffer
C-x C-o, to select the window showing the help buffer
q, (quit-window) will select the inactive minibuffer window

Best regards.

In GNU Emacs 29.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.33, cairo version 1.17.6)
 of 2022-04-20 built on miha-pc
Repository revision: 4714f34928c12cc9ebda7c115526db4aa87c0d51
Repository branch: tmp
Windowing system distributor 'The X.Org Foundation', version 11.0.12101003
System Description: Artix Linux

Configured using:
 'configure --without-libsystemd --with-native-compilation'

Configured features:
ACL CAIRO DBUS FREETYPE GIF GLIB GMP GNUTLS GPM GSETTINGS HARFBUZZ JPEG
JSON LCMS2 LIBOTF LIBXML2 M17N_FLT MODULES NATIVE_COMP NOTIFY INOTIFY
PDUMPER PNG RSVG SECCOMP SOUND SQLITE3 THREADS TIFF TOOLKIT_SCROLL_BARS
WEBP X11 XDBE XIM XPM GTK3 ZLIB

Important settings:
  value of $LANG: en_US.utf8
  locale-coding-system: utf-8-unix

Major mode: Fundamental

Minor modes in effect:
  tooltip-mode: t
  global-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
  blink-cursor-mode: t
  buffer-read-only: 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 mailcap yank-media rmc puny
dired dired-loaddefs rfc822 mml mml-sec password-cache epa derived epg
rfc6068 epg-config gnus-util text-property-search time-date seq gv
subr-x byte-opt bytecomp byte-compile cconv mm-decode mm-bodies
mm-encode mail-parse rfc2231 mailabbrev gmm-utils mailheader cl-loaddefs
cl-lib sendmail rfc2047 rfc2045 ietf-drums mm-util mail-prsvr mail-utils
iso-transl tooltip eldoc paren electric uniquify ediff-hook vc-hooks
lisp-float-type elisp-mode mwheel term/x-win x-win term/common-win x-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
simple cl-generic 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 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 dbusbind inotify lcms2 dynamic-setting system-font-setting
font-render-setting cairo move-toolbar gtk x-toolkit x multi-tty
make-network-process native-compile emacs)

Memory information:
((conses 16 59282 11257)
 (symbols 48 5734 0)
 (strings 32 16447 944)
 (string-bytes 1 548085)
 (vectors 16 11787)
 (vector-slots 8 271542 17553)
 (floats 8 21 25)
 (intervals 56 335 0)
 (buffers 992 11))