Quantum transport of charge or energy in networks with discrete sites is central to diverse quantum technologies, from molecular electronics to light harvesting and quantum opto-mechanical metamaterials. A one dimensional network can be viewed as waveguide. We show that if such waveguide is hybridised with a control unit that contains a few sites, then transmission through the waveguide depends sensitively on the motion of the sites in the control unit. Together, the hybrid waveguide and its control-unit form a Fano-Anderson chain whose Born-Oppenheimer surfaces inherit characteristics from both components: A bandstructure from the waveguide and potential energy steps as a function of site coordinates from the control-unit. Using time-dependent quantum wave packets, we reveal conditions under which the hybrid structure becomes transmissive only if the control unit contains mobile sites that induce non-adiabatic transitions between the surfaces. Hence, our approach provides functional synthetic Born-Oppenheimer surfaces for hybrid quantum technologies combining mechanic and excitonic elements, and has possible applications such as switching and temperature sensing.