It's also nice when this tool generates starter code for you, because every peripheral usually has a slightly different way to enable/configure/map their IO to a pin, and there's a global GPIO control interface, and there's a global power management control interface, and (... etc). You need to set all of the properties correctly simultaneously, or the connection doesn't get made. It's easy to miss one of them and be confused about why your signal isn't showing up.
Nordic's GPIO pin mux allows you to map any peripheral IO to any pin like an FPGA. There's one uniform interface for controlling this mapping, with no weird exceptions. I think that's why they don't have a tool like this -- it just wouldn't be all that useful, because remapping pins is so easy. When you're designing your board, you can, for example, wire up an SPI device to literally any pins you want, and then make it work in software later.
These tools can also useful for setting PLL divider values and configuring clock distribution, because this can get complicated: https://i.stack.imgur.com/e8CQw.png
But Nordic chips also tend to run at one officially supported clock speed, because their Bluetooth stack relies on it. So you don't really need the clock configuration GUI either.