Yeah. Precisely my problem with Nitrokey too.
If you can flash it, then so will a bad-guy one day. Not if, but when. You really can't say never anymore these days.
The flashing process is also annoying and fragile, I bought a couple of Nitrokeys for random testing and generally found myself haivng to repeat the process a couple of times before it finally worked.
Also, IIRC not all Nitrokeys have a secure enclave, a bunch just store secrets in software.