If Cypress doesn't provide pre-programmed FLASH parts, many distributors (I'm assuming based on your low volume you are using a distributor) provide this service for a small fee.
I used to work for a company that used a PSoC in their low-volume product line. The PSoC on the board had a programming header to be used with a MiniProg programmer/debugger. Our assembly line programmed the PSoC shortly before the End-of-Line testing.
The programming header was available for field-updates if needed.
Cypress does not offer pre-programmed parts for small quantities. Please check with third-party programming vendors who provide this service. You should be able to find them in the market. For example, our distributor Arrow has such a business.