How is this supposed to work and what makes it JetCore-specific?
I finally traced back the issues I reported to changes in hltL1SeededStartUpElectronPixelSeeds in HLT. 
There the number of seeds changes substantially and I suspect it's all due to this part of the code (the SeedFilter RecoEgamma/EgammaElectronAlgos/src/SeedFilter.cc is using SeedFromConsecutiveHitsCreator and in HLT case the region is the RectangularEtaPhiTrackingRegion)