You should likely set StartupWMClass property too. I use
[Desktop Entry]
Name=Avidemux Video Editor (Qt5)
Comment=Graphical video editing tool - Qt5 interface
Icon=org.gnome.Totem
Exec=/usr/local/bin/avidemux
MimeType=video/mpeg;video/quicktime;video/x-msvideo;video/x-anim;audio/x-mp3;audio/x-mp2;
Terminal=false
Type=Application
Categories=AudioVideo;AudioVideoEditing;
X-Desktop-File-Install-Version=0.23
StartupWMClass=avidemux3_qt5
as .desktop file while /usr/local/bin/avidemux contains just
#!/bin/bash
/usr/local/bin/avidemux3_qt5 > /dev/null 2>&1
exit 0
Works fine at least in gnome-shell 3.24 (didn't make the leap to 3.26 yet), but should work in 3.26 as well. If I need the debug output, I launch avidemux3_qt5 in terminal directly.