It looks like the original topics’ subject, which are comments or commented lines, lies upstream.
But there is more happening here. Here is some more information from my virtual machine about /etc/mkinitcpio.conf
1. compare arch with unsquashed RUAH iso manjaro-xfce-21.3.0-220617-linux515, manjaro/x86_64/rootfs.sfs
===> diff arch 01-iso\(619\).mkinitcpio.conf
55c55
< # Use this to compress the initramfs image. By default, zstd compression
---
> # Use this to compress the initramfs image. By default, gzip compression
57d56
< #COMPRESSION="zstd"
63a63
> #COMPRESSION="zstd"NOTE 1: This looks okay. It is the arch mkinitcpio.conf plus manjaro patch.
NOTE 2: Arch github matches an Arch virtual machine too.
2. Compare Manjaro iso with Manjaro after install
===> diff 01-iso\(619\).mkinitcpio.conf 02-install\(619\).mkinitcpio.conf
6,7c6,7
< # MODULES=(piix ide_disk reiserfs)
< MODULES=()
---
> # MODULES=(qxl bochs_drm virtio-gpu virtio virtio_scsi virtio_blk virtio_pci virtio_net virtio_ring)
> MODULES=(qxl bochs_drm virtio-gpu virtio virtio_scsi virtio_blk virtio_pci virtio_net virtio_ring)
19c19
< FILES=()
---
> FILES=""
52c52
< HOOKS=(base udev autodetect modconf block filesystems keyboard fsck)
---
> HOOKS="base udev autodetect modconf block keyboard keymap consolefont filesystems fsck"NOTE 1: HHHmmm, MODULES were added, FILES was change from array () to string “”, and HOOKS changed. Could not find changes at gitlab.manjaro.org.
NOTE 2: I created a topic regarding the bochs_drm. At this time, I removed bochs_drm from MODULES.
3. compare Manjaro after install with Manjaro after latest update
===> diff 02-install\(619\).mkinitcpio.conf 04-current\(0729\).mkinitcpio.conf
6,7c6,7
< # MODULES=(qxl bochs_drm virtio-gpu virtio virtio_scsi virtio_blk virtio_pci virtio_net virtio_ring)
< MODULES=(qxl bochs_drm virtio-gpu virtio virtio_scsi virtio_blk virtio_pci virtio_net virtio_ring)
---
> # MODULES=(piix ide_disk reiserfs)
> MODULES=()
19c19
< FILES=""
---
> FILES=()
52c52
< HOOKS="base udev autodetect modconf block keyboard keymap consolefont filesystems fsck"
---
> HOOKS=(base udev autodetect modconf block filesystems keyboard fsck)
67a68,73
>
> # MODULES_DECOMPRESS
> # Decompress kernel modules during initramfs creation.
> # Enable to speedup boot process, disable to save RAM
> # during early userspace. Switch (yes/no).
> #MODULES_DECOMPRESS="yes"NOTE 1: HHHmmm, MODULES removed, FILES changed back to array (), HOOKS changed, and MODULE_DECOMPRESS section added.
NOTE 2: The extra section was also mentioned by @anon51566685.
08/04/22: Captured output from the pacman command
...
core/mkinitcpio 31-2 31-2.0 0.00 MiB 0.05 MiB
...
upgrading mkinitcpio...
warning: /etc/mkinitcpio.conf installed as /etc/mkinitcpio.conf.pacnew
...It’s a mystery where these changes are coming from. 
If I can provide additional information to help, please let me know.
Moderater edit: Fixed broken link