So Neurally Connecting in my vision is, a chip in the head or device that lets you pilot the spidertrons remotely,
On a code level, the mod creates a temporary engineer, makes it the pilot, and makes you control the new engineer. When you leave the spidertron, it reverts control back to the original engineer, and destroys the temp engineer. As the temp engineer is inside the spidertron, you never see it, only the one (original) engineer exists at the visual level.
The Spidertron Enhancements 'Quick toggle' (Shift+Enter), only breaks the illusion of the neural connections. The created temporary engineer can run around, it doesn't break the neural connection, just quick toggle back into the spidertron and leave like normal.
You can have both mods, theres no conflict in code, I play with both, its more of a warning for to maintain realism.
You can quick toggle while neurally connected, but you shouldn't be able to
If this mod gets more downloads, maybe Xorimuth will make a patch that lets this mod stop quick toggle when Neurally Connected