Fuzzy 3.3V from MC34063
Layout is not optimized (it's very wide) can that play that significant role?


For a DC-DC, layout is everything.
Without a proper ground layout, input and output capacitors will be ineffective, and output voltage will be very noisy.

Without a ground plane, there will be large potential difference between different points labeled "GND" due to high di/dt currents flowing through inductive wires. This makes it impossible to measure anything reliably.


  Probe GND is max 7cm and I actually keep it close to probe not to make a loop to pick up noise.


You cannot measure anything in the vicinity of a DC-DC with the long ground clip. Lookup "Probe grounding and noise pickup" in this guide:

https://e2e.ti.com/support/power_management/simple_switcher/w/simple_switcher_wiki/2243.understanding-measuring-and-reducing-output-voltage-ripple

Conclusion: Your results are normal for a protoboard. If you want to build a prototype with realistic performance, do it dead-bug over a solid ground plane.