The problem is that if you open the VM Settings, and you "OK" them (you don't even have to touch the "Network" tab") anything attached to an IntNet, is going to automagically force-switch to "intnet".
However, if you click on that same network card in the Details pane (the new quick-set feature), you properly get all your IntNets, so that's a workaround (not really).
The output of the following command works as expected as well:
Tested it on an OSX, a Win10-64 and a Mint19 host. Problem started with 6.1.0b1 r133315, the first beta. Problem does not exist in the latest VirtualBox-6.0.13-133612-OSX, nor VirtualBox-5.2.33-133613-OSX.$ VBoxManage list intnets Name: VBoxIntNetwork <-- that's mine Name: Whonix <-- auto-created from an imported VM Name: intnet <-- the default