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Regarding Item1 (moving the heating coil to the outlet branch), this fails because SetpointManager:ReturnAirBypass assumes that only the supply fan is in the outlet branch after the bypass mixer. It subtracts the temperature rise across the outlet branch and makes that the adjusted bypass mixer temperature setpoint. So, anytime the heating coil is active, the adjusted setpoint will be lower which will cause the heating coil to continue operating. I do not see a workaround to this without modifying the code.

Regarding Item 2 (adding economizer), I don't have a definite answer, but my guess is that the OA controller and the RAB controller are fighting over the mass flow rate in the conditioned supply branch.

Regarding the EMS, I'll need to see the input file to attempt an answer (either post a link here, or open a helpdesk ticket).