Yes, the floating hidden window always pops up on whatever workspace I am currently working on.
I thought about automatically hiding it, when switching to another workspace, but have not yet come around doing this.
I use a simple script to start emacs in case I accidentally close it:
i3-msg 'exec emacs -name emacs-server'
i3-msg \[instance=\"emacs-server\"\] move scratchpad;
i3-msg \[instance=\"emacs-server\"\] floating enable;
sleep 1
i3-msg \[instance=\"emacs-server\"\] scratchpad show;
i3-msg \[instance=\"emacs-server\"\] move position 450px 0px;
i3-msg \[instance=\"emacs-server\"\] resize set 950 100 ppt
i3-msg \[instance=\"emacs-server\"\] scratchpad show;
The i3 config portion additionally has the key binding: bindsym $mod+less [instance="emacs-server"] scratchpad show
What if you're in a different workspace? Does the floating hidden emacs window follow you across workspaces?