Thanks, for the suggestions, but unfortunately both Unstoppable Wallet and Mycelium are mobile apps and I wasn't able to find any indication that crypto.com desktop app supports BIP-39 passphrase, just tried installing it and it only accepts the seed phrase when recovering wallets.
So the question is still there whether there are any open-sourced alternatives to Coinomi that will fit the bill.
I wouldn't recommend using desktop versions of multicurrency wallets because they often contain much more vulnerabilities than regular Bitcoin-only wallets, but the closest thing I found that meets your criteria is this one:
https://coin.space/. It has a Linux version, claims to have
"a BIP39 passphrase encryption on wallet creation, hardening the security of your wallet right out of the gate", and is likely open-source since I managed to find their GitHub page:
https://github.com/CoinSpace/CoinSpace. It could be that, however, they are confusing concepts by referring to a mere seed phrase as a wallet passphrase, so it needs verifying.
The other option is to switch to Windows or use emulators like Wine to run Unstoppable Wallet on a Linux machine. Or just ditch these pesky altcoins altogether.