Yes, I am seeing the same problem and it's causing me a few headaches. I tried running the Catalina version of productsign on Big Sur and it ran OK, but the resulting signed package still would not install on El Capitan.
Is it something to do with the format of the certificates? I got new ones when I moved my development environment to Big Sur, so that's another variable. Perhaps El Capitan doesn't support SHA256 hashes.