As of now, this is the whole thread at SSD maximal performance : native sector size, partition alignment - #30 by rustybird including changes made by @rustybird at https://github.com/QubesOS/qubes-linux-utils/pull/85
To make it really high level. And from my basic understanding as of now…
When installing the system, 3 modes are proposed.
LVM, creating fat filesystems where definite volume size is created. Those volumes are created per assumptions based on what the installer, and available tools, are able to get from the hardware.
Thin-LVM creates volumes without costs. This is really interesting because clones in Thin-LVM has no cost. So when you clone qubes, they have no cost until those volumes diverge. And there is no cost but the consumed space of those volumes (their content), where for clones, they refer to their original volumes and are qcow, so they diverge on writes on their thin-lvm themselves.
XFS/BRTFS/ZFS all have similar mechanisms, but since they are reflink, and files on the filesystem, the kernel drivers and pool implementation are the ones instructing how to deal with clones, and LVM mechanisms are not used there. Different implementations, different optimizations.
On file system creation.
For LUKS creation at install, if not hardcoded or properly detected (cryptsetup 2.4 if I recall well, not part of dom0 current fedora), the logical sector size is used, which is still 512 bytes instead of 4k. This is problematic for other tools which will reuse that assumption based on the block level of LUKS to creat the pools on LVM. Then, scripts are either reusing those logical sizes, or hardcoding sector size, depending of what types of volumes passed to the qubes. So rustybird patched volatile file creation so that qubes have the illusion of having a read+write root filesystem. But a problem persists to be able to replicate and tests optimized results. When installing templates at install, the root volume is not 4k. When creating service qubes and default appvms, private voumes are not created with 4k sectors. Some of those passed volumes into qubes (/dev/xvd*) require a partition table, which if misconfigured, will simply refuse to launch installed system.
This is where the discussion is stalled under https://forum.qubes-os.org/t/ssd-maximal-performance-native-sector-size-partition-alignment. @rustybird figured out where the problems lies. Proposed a fix for volatile volume creation and said it would be more complicated to fix private volume and root volume creation. Consequently, I do not know as of now what/how to patch a live iso at runtime (can invest time there but not now) to patch code used to private and root volume creation at install (phase 1 of installer) so that templates are decompressed on top of a correctly configured LUKS partition. But I do not know how to fix code for private volume creation, which happens through salt script against scripts and Xen block related code to actually create service app qubes and default qubes prior of booting into the system. Last time I checked, no qube were launching at boot.
That is the shortest version I can give on the state of that long thread over https://forum.qubes-os.org/t/ssd-maximal-performance-native-sector-size-partition-alignment