Make Gnome applications sidebar semi-transparent, and add blur with Blur My Shell Extension if you want to

gnome-transparent-sidebar.css

/* Mohammad Mahdi Tayebi
 * 
 * To apply transparent sidebar. copy this file into ~/.config/gtk-4.0/gtk.css and if 
 * you use adw-gtk3 theme you can add it to ~/.config/gtk-3.0/gtk.css as well
 * 
 * Use blur my shell extension to add blur effect behind the transparent part of windows
*/

/* Transparent Headerbar */
overlay-split-view revealer.raised.top-bar {
  background: alpha(@window_bg_color, 0);
  box-shadow: none;
}

overlay-split-view headerbar.titlebar {
  background: transparent;
  border: none;
  box-shadow: none;
}

/* Transparent Sidebar */
window {
  background: alpha(@window_bg_color, 0.8);
}

.sidebar-pane,
.sidebar,
.navigation-sidebar {
  background: transparent;
}

/* Global style */
.content-pane {
  background: @view_bg_color;
}

widget.background.overview {
  background: transparent;
}

/* Lollypop */
window>deck>grid>headerbar.titlebar>widget>widget>box>image {
  margin-top: -1px;
}

window>deck>grid>headerbar.titlebar>box> :nth-child(1) {
  margin-right: -44px;
  opacity: 0;
}

window>deck>grid>headerbar.titlebar>box> :nth-child(2) {
  margin-right: 34px;
}

window>deck>grid>headerbar.titlebar>box>.close {
  margin-right: 0;
}

window>deck>grid>headerbar.titlebar {
  background: linear-gradient(90deg,
      transparent 0%,
      transparent 220px,
      @headerbar_shade_color 221px,
      @headerbar_bg_color 198px,
      @headerbar_bg_color 100%);
  border-bottom: none;
}

/* Builder */
.org-gnome-Builder paneldockchild.center {
  background: @window_bg_color;
}

.org-gnome-Builder.workspace paneldockchild.start {
  background: transparent;
}

/* Speedtest (xyz.ketok.Speedtest) */
.horizontal>gauge.dl.horizontal>overlay>.background {
  background: transparent;
}

.horizontal>gauge.up.horizontal>overlay>.background {
  background: transparent;
}

/* Gnome Tweaks */
window>leaflet>box:last-child>scrolledwindow>viewport.frame {
  background: @window_bg_color;
}

.tweak-titlebar-left {
  background: alpha(@window_bg_color, 0.8);
}

/* Geary */
.geary-main-layout>leaflet>leaflet>box:first-child,
.geary-main-layout>leaflet>leaflet>box:first-child>headerbar {
  background: transparent;
}

/* Rhythmbox */
window box:nth-child(2) paned:nth-child(3) paned:nth-child(3) box:nth-child(2) {
  background: @window_bg_color;
}

window box:nth-child(2) paned:nth-child(3) box:first-child paned grid .sidebar-toolbar,
window box:nth-child(2) paned:nth-child(3) box:first-child paned grid .sidebar-toolbar button {
  background: transparent;
}

window box toolbar {
  background: transparent;
  /* Comment this if you don't want transparency on rhythmbox topbar */
}

/* Disks */
window>deck>box>leaflet>box:nth-child(3)>stack>statuspage>scrolledwindow>viewport.frame,
window>deck>box>leaflet>box:nth-child(3)>stack>scrolledwindow>viewport.frame {
  background: @window_bg_color;
}

window>deck>box>leaflet>box:nth-child(1)>scrolledwindow treeview.view {
  background: transparent;
}

window>deck>box>leaflet>box:nth-child(1)>headerbar.titlebar.windowhandle {
  background: transparent;
  border-bottom: none;
}

/* BkackBox Terminal */
#blackbox-main-window {
  background-color: transparent;
  /* Unless transparency won't work */
}

#blackbox-main-window headerbar {
  background-color: rgba(20, 21, 35, 0.85);
}

/* Ghostty terminal */
window.terminal-window {
  background: transparent;
}

window.terminal-window .top-bar {
  background: alpha(#1e1e2e, 0.8);
}

window.terminal-window .top-bar windowhandle {
  background: transparent;
}

/* GNOME Text Editor */
dialog-host>widget>widget>toolbarview>stack>tabview>widget>page>box>overlay>box>scrolledwindow>textview.editor.view {
  background: alpha(@window_bg_color, 0);
}

dialog-host>widget>widget>toolbarview>stack>tabview>widget>page>box>overlay>box>scrolledwindow>textview.editor.view>border,
dialog-host>widget>widget>toolbarview>stack>tabview>widget>page>box>overlay>box>scrolledwindow>textview.editor.view>border>gutter,
dialog-host>widget>widget>toolbarview>stack>tabview>widget>page>box>overlay>box>scrolledwindow>textview.editor.view>border {
  background: transparent;
}

any ideas to make this work with Flatpaks?
I've tried setting the gtk-4.0 and gtk-3.0 folders using Flatseal but I've had no dice with it