Not all. Some parts require proprietary tools to build a full firmware image for the chip, to debug the part, or to write to the target's onboard flash. Thankfully, these are all getting less common -- but there's still some out there. For instance, the Cypress PSoC requires Cypress's tools to generate configuration data for the part's configurable digital blocks -- there isn't enough information in the reference manual to do this yourself.
At least the Cypress tools are freely available and well documented. I have built probably 7-10 products using the PSoC, the tools worked well, resulting firmware solid. Don’t know why you would use Cypress as your example?
Because you can't not use their tools. The register TRM is deficient on some details of the UDB structure like routing, which is essentially mandatory for use the part. (You can technically program the part using only hard peripherals and GPIOs, but that leaves you with a crippled microcontroller.)
