I don't fully agree with the reasoning presented in #21889 (comment) but let's be OK for now.
Adding a check like done here in ParameterBag looks wrong to me. ParameterBag does not deal with env vars, why should it care at all now? There is a responsibility mismatch to me.
I'd way better go with #21889 for now (the deprecation of getEnvParameters is nice and should be kept.)

Getting parameters automatically created from SYMFONY__ env vars is what we are deprecating to me. How would you detect that the user is relying on the fact we transform env vars into parameters than doing this check in ParameterBag::get()? We could store the env-related params in a prop when setting them from Kernel::getEnvParameters() instead of reversing the transformation, but it would still involve to do this check here.

I don't know yet, but right now, the drawback of this implem (SRP break) is worse than the drawback of the implem in #21889 (a theoretical false positive).

We'll remove this check in 4.0 as well as the practice, IMHO we don't care but of course I would go for any better alternative.