Yes, it can be set in iTerm's Preferences → Keys → Remap Modifiers
Next, in the same Preferences Pane, select Key Bindings Tab.
From there, you will see all the currently defined key bindings. If Control-Tab isn't defined you can create a new one, however this is a clean install and this is what's shown by default.
Double click on the "Action" description to modify the behavior.
It will bring up a (long) list of actions you can assign to the keybinding. (I selected "Cycle Tabs Forward")
This will configure iTerm to accept the left ⌘ Command as ^ Control and is limited to iTerm only. ⌘ Command ⇨Tab still works, but within iTerm you must use the right ⌘ Command. Outside of iTerm, everything will function as normal.
If you're using Catalina, you will have to give Accessibility permissions to iTerm under System Settings → Security & Privacy → Privacy Tab → Accessibility if you haven't already done so.