Actually, turns out that if you keep your keymap switcher mapped on the base layer of both keymaps, and you don’t have anything mapped differently on any layers of the second keymap (COL), then you don’t need to enable any layers on the second keymap at all! The layers from the source (QWR) will still be available and activate as normal with them disabled on (COL)! 
In my first testing, I only needed to enable a single extra layer because I originally had my keymap switchers on the Fn layer (the rest of the layer’s keys were empty on second keymap).
Here’s all you need to switch from QWR —> COL 
:
NOTE:
I found a backlighting/touchpad bug while testing this stuff. With the minimal setup shown in the above image, when switching to the COL keymap, the right-half LEDs only illuminate for the keys that are mapped on the COL keymap. The rest remain dark, but the left keyboard half stays fully lit up. If I tap a layer switch key, or if I detach/reconnect the touchpad, it resolves it.
FW v16.2.0 #17c7979
Started the layout by resetting the userConfig, deleting all the default macros and keymaps (except QWERTY), and then adding an Empty keymap to build the COLEMAK overlay. Then added the $onKeymapChange COL macro. Pretty sure that’s all the changes made.