Attach the plates pbs to the longer beam before lifting them up, so it should be fairly easy to fit the shorter beam afterward. Push in the beam, clamp the plates with the shorter beam in between using a quick clamp. Check to ensure everything is straight and neat, screw in a few anchor screws for an initial fixation.
Yes, the 5cm shift can complicate things.
Especially if you're trying to maximize the width for the roof trusses with 1200mm in each section. Then it gets a little complicated when the flooring joists don't align with where you want to lay the floor particleboard, etc.
High-quality particleboard doesn't need to be joined over the beams?
Nor do floorboards that are tongue-and-groove on all sides.