Future all battery equipped fleets can certainly avoid undesirable dual electrified areas at the changeovers. The systems have very different earthing strategies. The rails in 750VDC only areas are not bonded to earth. They remain isolated from ground on plastic pads and clip inserts to encourage return current to remain in the running rails. In 25kVAC everything metalic in the corridor, including stanchions, electrical cabinets, station structures, bridge components etc, must be earthed for touch potential safety. Rails are also earthed; normally the 'traction rail' as opposed to the 'signalling rail', where that needs to be electrically isolated for track circuits. In axle counter areas, all rails can be frequently bonded to each other, and earth.
In dual electrified areas, the necessary 'compromise' is that comprehensive earthing must be installed for safety, which provides very many potential 'escape paths' for the DC return current to leak out, leading to the stray current taking alternative routes back to the substation, risking corrosion of metalwork and underground utilities en route, both within and outwith the railway boundary.
On Thameslink, I think the sheer complexity of the core changeover area, with all the metal-framed high value buildings, city streets and railway structures nearby forced the particular complicated switching solution to derisk this. In a rural location (not on a metal bridge!) this would be less of a concern and there are techniques for reinforcing the preferred return path with some parallel cabling to ensure the lowest possible loop resistance. This can reduce the leakage, but can't eliminate it entirely, as current spreads out along all possible paths, proportionally according to their resistance, so there's always some risk, more so under fault conditions where a preferred return path is interupted.