Self-organisation is in no way a bottom up process. All humans are involved in interaction, and the results that emerge are the results of self-organising processes, whether you are a top manager or lower in the hierarchical ranks.
It is not very accurate to call self-organising a “bottom up” approach or process. To me, a bottom up process is where there is activity amongst those lower in the hierarchy or closer to the front line who feed ideas or a new process up through the hierarchy. A bottom up process can happen because it’s been designed by the top managers e.g. a series of facilitated focus groups, or it can happen more informally e.g. where a problem is solved or a new process is established at one site and then the results are seen by those higher in the hierarchy and the new process is implemented at other sites.