As the error message suggests, some properties of the 'Sim' command cannot be altered when the model is in compiled state (which is essentially the case when 'FastRestart' is turned on). For example, you cannot perform 'save' operations in this mode. As a workaround, you can turn off the FastRestart mode and set these options using set_param. After doing so, you can turn on FastRestart and simulate using the 'sim' command. Please find the modified code below:
load_system(mdl);
set_param(mdl,'FastRestart','off');
set_param(mdl,'SaveFinalState','on','FinalStateName','xFinal','SaveFormat','Structure');
set_param(mdl,'FastRestart','on');
% Create a SimState at the final time of 0
% (as soon as the simulator starts)
simOut = sim(mdl,'StopTime','0');
set_param(mdl,'FastRestart','off');
set_param(mdl,'StartTime','0','SaveFinalState','off','StopTime','5');
set_param(mdl,'FastRestart','on');
% Adjust simulator over iterations
for i = 1:100
simOut1 = sim(mdl,'LoadInitialState', 'on', ...
'InitialState', 'simOut.xFinal');
end