And if you really have to be stealthy there with this submarine, send another crew with mapping capabilities using a decoy mission in which you don't have to hide that you are passing by.
I don't know precisely how secure boot works under fedora, but you can have FDE with swap just fine in Linux. A swap partition can live inside a LVM logical volume.
For secure boot I would guess you could have the EFI partition signed/validated with the TPM.