I don’t understand what you are saying, and what is your concern.
You meant that the two separated keyboards are problem to have another layer?
I have the external split keyboard called Moonlander running with the QMK. And the left and right keyboard PCB are connected with a cable from the both controllers. I haven’t openned the Moonlander. So, having the 2 controllers are my assumption.
And here is my current 34 keys layout. You see the “1 hold” key on the left bottom. The key changes the layer from layer 0 to layer 1 when holding the key. It’s like Fn key on teh current Framework Laptop. The key uses the feature of “MO (layer)”.
QMK Firmware - feature_layers
MO(layer) - momentarily activates layer. As soon as you let go of the key, the layer is deactivated.
And I am also assembling another external split keyboard called Sweep Bling LP now. The keyboard has 2 controllers (in my case, the RP2040 based controllers to run QMK on it). This picture on QMK repository shows the 2 controllers on the both PCBs.