It appears llc gives preference to the default target datalayout whereas opt gives preference to the module datalayout. Is there a reason they behave differently?
From llc.cpp:
// Add the target data from the target machine, if it exists, or the module.
if (const TargetData *TD = Target.getTargetData())
PM.add(new TargetData(*TD));
else
PM.add(new TargetData(&mod));
From opt.cpp:
// Add an appropriate TargetData instance for this module.
TargetData *TD = 0;
const std::string &ModuleDataLayout = M.get()->getDataLayout();
if (!ModuleDataLayout.empty())
TD = new TargetData(ModuleDataLayout);
else if (!DefaultDataLayout.empty())
TD = new TargetData(DefaultDataLayout);
if (TD)
Passes.add(TD);