I really enjoy the planning and implementation of what you describe. One thing to consider, is that when the train enters the "dead" control section, and then power is re-applied, the E-unit will want to cycle.
Option 1 - You can switch the e-unit to forward only
Option 2 - If your prefer to retain the e-unit cycling ability, the starting/stopping would be controlled by switching the center rail power on and off (rather than control via the outside ground rails). You would need to insulate the center rail, and install a resistor that maintains a minimal amount of power when the power is "off" i.e., not enough to make the train move, but enough that the e-unit will not cycle. Page 31 of the 1954 Lionel operating manual describes this. Pages nearby discuss other "old school automatic operations."