One of the saner reasons for this structure is that the non-profit owns the things the for-profit works on. If the for-profit goes under, all things are still owned by the non-profit, so some large tech company can't swoop in and yoink anything available.
This includes any and all data generated by the for-profit, which means your data is "safe".
There are two separate entities: the raspberry pi foundation which is the charity and unchanged, and the raspberries pi holdings company which has always been the business side of the project. The corporation contributes to the foundation a significant amount of money which is not changing. The charity is the majority stakeholder in the company.