"As far as I know, MacroVision works by messing with the VCR's AGC (Automatic Gain Control) recording circuitry. Since a modulator doesn't record, there is no AGC. Once modulated to an RF signal, the MacroVision 'signal' is lost, and not re-inserted."

Unfortunately this is incorrect, the modulator will pass the macrovision encoded signal to the VCR, where it will be demodulated back to baseband (with macrovision intact) then remodulated onto ch3 again by the VCR. The VCRs AGC is in the circuit now, and will be affected by macrovision. Your first diagram is the way to go.