Ubuntu – “Open containing folder” in Firefox does not use the default file manager

It's a longstanding issue which was reported here for Chromium. At that time, there was no way to select an individual item in a folder, only open the folder, and so was marked as fixed, with half of it being implemented. However, according to this bug report, Nautilus has implemented the ability to select individual items, and it seems so has Dolphin (KDE equivalent of Nautilus). Perhaps it's time to open a new bug on this.

This is an awkward, quick and dirty solution you advocate. You Can't use Nautilus anymore. If it's your intention then it's better to remove it for good.

$ sudo apt-get remove nautilus

Otherwise I believe the proper solution is to modify the defaults.list file located in /usr/share/applications as suggested here.

In Ubuntu Xenial 16.04 I did comment out the original line and replaced nautilus with nemo e.g.

#inode/directory=nautilus-folder-handler.desktop
inode/directory=nemo.desktop

Then just restart Firefox and you will be OK ...