> but whole content (not-white pixels) are placed in lower, left 

Does your PNG image have a virtual canvas associated with it?  Add +repage.
The logo image does not have a virtual offset so no +repage is needed:

  convert logo: logo.png
  convert logo.png logo.pdf
  compare -metric mae logo.pdf logo.png null:
  0 (0)

A mean absolute metric of 0 means there was no loss of information in the
image pixels.
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