Add back +rootio for HepMC3, requested by Jacek M. Holeczek. +pythia has to be removed from ROOT because it's impossible to satisfy the cycle ROOT depends on Pythia8 who depends on HepMC3 who depends on ROOT.
Other fixes: -fPIC is needed for some dependencies of pytorch on Alma 9, dd4hep installing to lib64 on Alma 9, etc.