After launching from the KSC, the crew (and thus control and Local Command capability) abruptly disappear somewhere between 600m and 700m ASL.

This does not occur if the command pod is inside of a payload faring, but happens immediately once the faring is deployed.

This only occurs when RemoteTech is installed.

My guess is that this is a problem resulting from a single part having both crew command and data transmission ability. Once an antenna reaches a certain range, remote control is disabled. Perhaps the crew command module is being disabled as well? This could be easy to fix, or, depending upon how RemoteTech control enabling/disabling works, could be a lot harder than it appears.

Solved in commit 470750b

Summary: the Communotron 16, from which the config values were sourced, has ModuleSPUPassive and ModuleRTAntenna. In order to provide only the data transmission capability and not range-limited probe control, ModuleSPU and ModuleRTAntennaPassive are required.