This update adds a requested feature to be able to place command blocks while in edit mode. This feature is disabled by default but you can enable it by setting the option "command-substitute" to a valid block from https://hub.spigotmc.org/javadocs/spigot/org/bukkit/Material.html

Due to the way the internals of the server work, a player cannot place a command block unless they are a real OP, even if they have the minecraft.commandblock permission. To get around this, the command-substitute option was created. Whatever block you put in here will be replaced by a command block when placed in edit mode.

There is no easy way to get the direction a block should be facing that I can see, so I've hacked together a way to do it. If you experience problems getting a command block to face the correct direction, set the command-substitute option to a block that also naturally has a directional property, like a piston. If you use a block that cannot face all directions, like a torch, (torches can't have BlockFace.DOWN I believe) you will not be able to place command blocks facing down.

If you use a tile entity as the substitute block, such as a skull or a chest, you may get a scary message like this:
This message is harmless, (we just created the block, there is no valuable data to be damaged) but you may wish to set it to something without extra data like a piston to avoid getting this message.

As usual, report any bugs or features you'd like to see.