There are downsides to 100% Pex.
First, it couples noise much better than flex. This is important with the pump connections.
Second, it can be very difficult to get fittings on Pex to align with the fittings on a faucet in the tight space behind a sink.
Finally, Pex can result in stresses on fixed fittings and valves since it is stiffer. Not as stiff as pipe, but you don’t want a horizontal run bouncing and applying forces to a fixed fitting.
My 2 cents is to leave the flex on the pump and faucets, and possibly some places on the control panel, while using proper fittings and adapters. Also to anchor Pex near fixed connections and be sure it approaches the connection as close to 90 degrees as possible to minimize torque.