Standalone execution is our default boot for the F28069M LaunchPad. Make sure that you have the LaunchPad board selected in the configuration parameters of the model and the the "boot from flash" option is selcted in the build options. If "boot from flash" is not selected, we load in RAM which has the advantage of loading fast and executing fast but the code vanishes on a power cycle.
We don't touch the OTP with our default linker command files.
To be noted: When the JTAG part of the LaunchPad is not powered, (jumper1, 2 and 3 removed) and the board is powered externally (not from USB but maybe from a booster pack via the booster pack header pins), the floating reset pin may cause the board not to boot on a power cycle. In this case, you need to open the switch corresponding to the TRSTn, so the board is able to boot on a power cycle. Make sure to reconnect TRSTn every time you want to reprogram the board via USB. To start with, I recommend testing standalone while the board is powered from USB, with USB power cycles, this should work out of the box.
I hope it helps,