A set of transit proposals aimed at eliminating duplicate work between the MTA’s subsidiary agencies would limit city transit boss Andy Byford’s control over the system, rider advocates complained after the city officials were briefed on the report Friday.

The proposals, in a $4 million report prepared by the consulting group AlixPartners — a summary of which was publicly released Friday — recommend relocating all budgeting, human resources, legal, engineering, procurement, and external communications operations to MTA headquarters — mimicking proposals Gov. Andrew Cuomo put forward when Mayor Bill de Blasio signed onto congestion pricing in February.

“Today is the beginning of a new, modern MTA – one that delivers better service, completes projects on time and on budget, and uses its resources effectively and efficiently,” MTA Chair Pat Foye said in a statement.

By consolidating “duplicative” operations, the MTA expects to shave hundreds of millions of dollars off expected future operating deficits. The report proposes at least four new high-level positions: a Chief Operating Officer, a Chief Engineering Officer, a Chief Accessibility Officer, and a Chief Transformation Officer responsible for enacting the report’s recommendations.

But rider advocates were livid about the timing and contents of the plan, asserting that it would dis-empower popular city transit boss Andy Byford by moving key pillars of his Fast Forward subway and bus reboot out of his jurisdiction — the day after agency officials announced that subway performance has hit six-year highs on his watch.

The MTA attributes the uptick in service to Gov. Andrew Cuomo’s “subway action plan,” which went into effect six months before Byford came to New York, as well as Byford’s Save Safe Seconds program, which focuses on re-timing signals to increase train speed limits. Yet the Alix report claims speeds haven’t been reviewed in “decades.”

“It seemingly ignores improvements already underway from the Fast Forward plan, in the areas of accessibility and on time performance thanks to signal re-calibration and improved system maintenance,” said Lisa Daglian of the Permanent Citizens Advisory Committee, the MTA’s in-house advocacy org.

“Every bit of Fast Forward is more or less removed from Byford’s control,” said Tri-State Transportation Campaign Executive Director Nick Sifuentes.

But Foye insisted the British rail exec would maintain an active role in signals and other Fast Forward projects, working in conjunction with headquarters.

“Andy Byford is going to continue having the role he has today, which is driving customer service and performance,” he said.