I'm not sure if this is the kind of thing you're looking for or not, but here's a situation I encountered in just the last couple of days.
I have a new workstation PC I just recently put together. It's currently running Ubuntu 16.04 LTS but I plan to switch over to Arch Linux in the near future. Because I want to use LUKS (a.k.a. full disk encryption) and ZFS (and multiple ZFS pools) on it, I decided to work through the installation procedure on a laptop first (just to make sure I've got the steps down right -- an installation w/ the root filesystem on ZFS is "non-standard", and LUKS throws additional issues into the mix) before I wipe out my primary work machine.
First, by default, the LUKS setup only supports "unlocking" a single encrypted drive at boot. Since the laptop has a pair of SSDs (in a ZFS mirror), I need to unlock both of them (and my workstation has an NVMe, two SSDs, and two HDDs, so that'll be an even bigger problem!). I had to "hack on" the initramfs stuff so that I could unlock both drives when the system boots up.
In addition, I have several Yubikeys and wanted to use them with LUKS. I set them up in Challenge-Response mode, programmed them with a "secret key" that I generated, and then came up with a (relatively) short(er) passphrase that I can use to unlock the disks. I also had to create a custom (initramfs) "hook" to prompt for my passphrase, detect if a Yubikey is attached and, if so, send the "challenge" to the Yubikey, receive the response from it, and use that to unlock the disks. If a Yubikey isn't attached, then I have to provide a (much longer, more secure) "backup" passphrase to unlock (each of) the disks.
On the laptop, this means I can enter in my (relatively) short(er) passphrase once and unlock both disks. On my workstation, it means I'll enter it once to unlock all five disks. The alternative would be to type in my much longer, more secure passphrase FIVE separate times every time I boot the system up.
None of this was very hard or time consuming, but it was necessary in order to meet my exact goals and I'm glad that Linux allows me the opportunity to do exactly this type of non-standard stuff.