Add below piece of code in your 'StopFcn' callback function. When the simulation is completed, it will open and autoscale all the scopes in the model.
[EDITED TO WORK FOR MULTIPLE INPUT SCOPE]
bh=find_system(gcs,'FindAll','on','BlockType','Scope');
for x=1:length(bh)
set_param(bh(x),'Open','off');
end
for x=1:length(bh)
set_param(bh(x),'Open','on');
fh=gcf;
AxesInScope = findall(fh,'type','axes');
for y=1:length(AxesInScope)
set(fh,'CurrentAxes',AxesInScope(y));
xlim('auto');
ylim('auto');
end
end