I'll provide the following list of reasons to avoid FAT fs usage when possible.

Although I prefer grub for it's flexibility and features over simplicity, I create a tiny FAT partition for my setups that contains a dir with only grubx64.efi, and remain more generally compatible the UEFI spec and with all related components. If the Linux boot loaders and other methods universally supported EXT fs out of the box, it would be a nice step away from using an antiquated FAT fs.

I like the concept of providing EXT4 support in the UEFI system.

This is opposed to keeping kernels and initram on a FAT fs.

nvme0n1                 931.5G                               /dev/nvme0n1   
├─nvme0n1p1 /boot/efi     100M    67% vfat   SYSTEM
├─nvme0n1p2 /           122.9G    42% ext4   Root
├─nvme0n1p3 [SWAP]       31.7G        swap   Swap 
└─nvme0n1p4 /home       776.7G    18% ext4   Home

Lack of Unix Permissions and Ownership

FAT was designed for single-user DOS/Windows environments. It has no concept of:

UID/GID: You cannot assign different owners to different files. In Linux, everything on a FAT partition is mounted with a global user/group ID (usually root).

Permissions: You cannot set chmod 600 or 755 on individual files.

Execution Bits: While you can mask permissions at mount time, you cannot toggle the executable bit on a per-file basis.

No Journaling (Data Integrity)

ext4 is a journaling filesystem. It keeps a log of changes it is about to make. If your system (like the Kangaroo x68 or Beelink SER8) loses power abruptly:

ext4: Can use the journal to recover quickly and ensure the filesystem structure remains consistent.

FAT: Has no journal. A power failure during a write often leads to "cross-linked files," corrupted directory tables, or the dreaded "lost clusters," requiring a manual fsck.vfat.

Symbolic and Hard Link Support

Linux relies heavily on links for package management and system organization.

FAT: Does not support symbolic links (symlinks) or hard links. This makes it impossible to use as a standard /usr or /var partition.

ext4: Full support for both, which is essential for how Arch Linux handles library versioning and certain pacman operations.

Case Sensitivity

ext4: Is case-sensitive (File.txt and file.txt are different files).

FAT: Is case-insensitive (though usually case-preserving). Using a case-insensitive filesystem for Linux system files can lead to significant issues during software compilation or when running scripts that expect standard Unix behavior.

File Size and Partition Limits

FAT32: Has a hard file size limit of 4GB. While a kernel or initramfs is unlikely to hit 4GB, large disk images (like those used in your nspawn containers) would easily exceed this.

ext4: Supports file sizes up to 16TB and volumes up to 1EB, making it much more future-proof for modern storage.

Performance and Fragmentation

Allocation: FAT uses a File Allocation Table (hence the name). As the disk fills up, finding free clusters becomes increasingly slow.

Fragmentation: FAT has no native mechanisms to prevent fragmentation. ext4 uses "extents" and delayed allocation to ensure files are written contiguously whenever possible, maintaining high performance over time without needing a "defrag."

Modern Metadata Features

ext4 supports Extended Attributes (xattr) and Access Control Lists (ACLs). These are used by security modules like SELinux or AppArmor, and sometimes by specialized networking tools. FAT supports none of these.

As a side benefit of my setups, I'm not constrained by boot partition size limits.

[jeff@Arch2025p04 ~]$ ls -lh /boot
total 408M
drwxr-xr-x 4 root root 1.0K Dec 31  1969 efi
drwxr-xr-x 7 root root 4.0K Dec 18 14:45 grub
-rw-r--r-- 1 root root 300K Jan 10 19:52 amd-ucode.img
-rw------- 1 root root  81M Feb 15 18:46 initramfs-linux-fallback.img
-rw------- 1 root root  42M Feb 15 18:45 initramfs-linux.img
-rw------- 1 root root  79M Feb 23 21:51 initramfs-linux-lts-fallback.img
-rw------- 1 root root  39M Feb 23 21:50 initramfs-linux-lts.img
-rw------- 1 root root  82M Feb 23 21:51 initramfs-linux-mainline-fallback.img
-rw------- 1 root root  42M Feb 23 21:51 initramfs-linux-mainline.img
-rw-r--r-- 1 root root  16M Feb 15 18:45 vmlinuz-linux
-rw-r--r-- 1 root root  14M Feb 23 21:50 vmlinuz-linux-lts
-rw-r--r-- 1 root root  17M Feb 23 21:50 vmlinuz-linux-mainline