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Welcome in the forum and in the fascinating world of PSoCs!
In both cases the underlying microcontroller is an ARM M0 processor. The difference between the two prototype kits is that the -049-41xx contains fewer hardware components (no UDBs).
I (personally) do not recommend these prototype kits as entrance into the PSoC world since they do not allow for debugging and require a bootloader/bootloadable program. I do recommend the development kits as CY8CKIT-042 or (even better) the CY8C-044 kit. They allow for debugging and when the project has been tested it can be programmed (with small modification) into one of the CY8CKIT-049-4xxx prototype boards.
The reason I am keen is it has fewer components, and I can easily integrate the board into my product. I could also use the attached USB-Serial bridge to re-program the device while in the field. The product I am designing is meant for use industrial use, and is basically a motion control system, used to control a stepper motor.
However the development kits you suggested also looks interesting...