Documentation: For now, recommend producing .dst files for HLT1 and HLT2 when running over MC

As far as I understand from Chris Burr, for now the recommended method when producing Upgrade MC is to produce .dst files from hlt1 and hlt2, such that the truth information can still be propagated. This MR adds a warning to give a heads-up to people that they should do this; I do not think it makes sense to modify the options file or add another options file (but happy to be corrected). In case this advice is outdated, this would be a good place to discuss the current best advice.