Helo @Poley ,
Still no news from the RAppID BL Team.
I have investigated what you reported here ( the download code check and the delay) so let's take them step by step.
1. When the Download code after build was not checked, the RAppID header was not inserted in the generated code.
To solve this, please update the attached tlc file. For that, please type in MATLAB the command
winopen(fullfile(mbd_find_s32k_root, 'mbdtbx_s32k'))
This will open a Windows window where you have to replace the attached file.
So make sure that the Serial option is selected in the Config block, even if the option is greyd out ( first check the Serial option and then uncheck the Download code after build option).

2. For the APPDELAY, at first I thought that the MBD Toolbox is not updating the value in the generated code. But proved out that we do update the value in the generated code, so the same, I have requested some clarification from the RAppID BL team.
Hope this helps,
Marius