You found a bug in the software which we will fix in the next support package update. External mode is assuming GPIO29 and 28 are used for serial communication even though we set different GPIOs for serial communication in SCI_A tab of configset.
As a workaround you can update registerSCIpinAssignmentExternalMode.m as below:
At line number 8, update GPIO pin to 43 instead of 28: GPIOPinUsed = 'GPIO43'; %SCI Rx pin on F2837xD Launchpad
At line number 11, update GPIO pin to 42 instead of 29: GPIOPinUsed = 'GPIO42'; % SCI Tx pin on F2837xD Launchpad
This file should be in the path SUPPORT_PACKAGE_ROOT\blocks\masks. For Example, C:\ProgramData\MATLAB\SupportPackages\R2017b\toolbox\target\supportpackages\tic2000\blocks\masks\registerSCIpinAssignmentExternalMode.m.
Take a backup before updating this file and use this workaround at your own risk till we update the support package.
Hope this helps, let us know.