I could solve the same problem with editing ~/Library/Preferences/com.apple.symbolichotkeys.plist.

First, you need older version of MacOS from which you copy the plist with the middle click button enabled. Copy the plist with middle click button (old plist) and the plist of MacOS Sequoia (new plist) anywhere you want.

Second, you have to download PropertylistEdi-tan. https://anikikobo.com/archive/PropertyListEdi-tan150_a.zip. Unzip and place it anywhere you want.

Open old plist and new plist with PropertylistEdi-tan and save them as XML.

Open both xml with text editor, search the word 'button' in old plist, copy all the keys contains 'button' to new plist and save it.

Open editted new plist with PropertylistEdi-tan and save it as Binary, then copy it to ~/Library/Preferences/ , and reboot.

This worked, at least for me.