You can layer them however you want, so you can slap luks on the physical drives, or the mdraid, or the individual LVM volumes as you do right now. If the entire setup is either locked or unlocked, luks between the raid and LVM PV makes sense. Having luks on the individual LVs have the advantage that you can have your data partially unlocked.

2FA is complicated. You can use a second factor like, you need to enter both a password and be in possession of the flash drive, but you can't do it with the standard TOTP codes because you need the key to validate them in the first place.

One thing you can explore is TPM: the computer can detect if it's been tampered with, and if all checks out, it will unwrap the key. You can add a password or flash drive as a second factor. There's also the whole smartcard rabbit hole.

What exactly are you unsatisfied with? I think that's a better starting point to advise on.

Encrypt the boot drive, and use dropbear ssh in initramfs to be able to unlock it over ssh during boot. Then set up your data drives however you want, and use a key file on your boot drive to unlock them, once you've unlocked it. All drives are encrypted when your machine is off, and you only need one password you can enter remotely to unlock the whole thing.

Here's a good resource on how to do the initramfs part https://www.arminpech.de/2019/12/23/debian-unlock-luks-root-partition-remotely-by-ssh-using-dropbear/

Also, when you update the kernel you have to rebuild the initramfs with sudo update-initramfs -k all -u, or it won't be able to boot to the new kernel.

I've found it to be a super reliable setup.

TPM & secure boot. Look into sbctl for secure boot if you’re not on something that uses the signed shim like ubuntu. I know some hate secure boot but storing the unlock key in tpm is at least much more secure than having the key sitting on a usb drive

Tang - network based unlock. If you have a separate raspberry pi or something you can set it up as a tang server. You’ll want that thing encrypted too, can set that up to require manual unlock so if someone boosts your servers the tang server never comes up, storage server won’t either

Or just manually unlock the server with a password every boot?

That’s roughly my prioritized/preferred list

First off if I remember correctly there was some people complaining they lost everything with XFS so be careful.

Secondly, could you use a iSCI volume? It would limit it to your laptop only but you should be able to encrypt it all.

The other option is to encrypt some sort of file that holds your data.