finetune throughput options

Change a couple things to make options work properly with new benchmarking scripts in lhcb-core/lhcb-benchmark-scripts!3 (merged)
Also move default file to newer ft decoding version v4.

Edit: forgot to mention, this also introduces the LoKi Filter to filter out events with no PVs.

@cattanem WIP as these will for sure change the corresponding ref files as this changes the input file.