The Gaussian beam with the spot diameter of 200 mm is incident onto the circular receiver aperture (diameter of the aperture is 50 mm). A large part of the incoming Gaussian beam will be clipped by the receiving aperture. In that case, the "Gaussian tails" will be cut out forming a truncated Gaussian beam.
Should I consider this truncated Gaussian beam as a flattop beam?
After the 50 mm aperture, I am going to use a set of lenses to manipulate the diameter of this Truncated beam in order to couple it into the fiber.
If the fibre is at the focus or waist of your lens system, then the truncation of the Gaussian will result in sidelobes outside the main lobe at the focus.
I can't tell if your pictures are amplitude or intensity. You will know. Do a Fourier transform of the truncated amplitude (assuming it is at a waist where the phase is flat) to see what the pattern will be like at the focus/waist. Excel or Matlab might be able to do this. The size of the sidelobes depends on the height of the vertical step, so it is not quite so bad as a flat-top beam, but it is a long way from Gaussian. You will get a bit more power in the main lobe than for a flat-top, but the lobe will be a little wider.
Chapters in antenna design books on reflector antenna design will have graphs showing the relationship between the intensity at the edge of the aperture and the sidelobes in the far-field. I think the same applies from your aperture to the focus - they are transform pairs.
You can add the two beamshapes - add the root intensities, or amplitudes.
The beamshape will be 2/3 of the beamshape of a flat-top plus 1/3 the beamshape of the rounded top, approximately.
Alternatively it is the beamshape of a Gaussian convoluted with the beamshape of a square-top (all using amplitude).
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