Via the Spec:
"A number of large stumbling blocks were at issue at that point, sources said, including whether the HSR or Metrolinx would operate the LRT and whether the province would build the entire proposed route from McMaster University to Eastgate Square."
There's a seldom-discussed potential outcome: Hamilton gets LRT, the province covers capital costs and Metrolinx operates the LRT system — so the associated revenue vanishes from the HSR’s coffers.