update broke homebrew and flatpak in PATH

After updating my system and rebooting, I can no longer use brew (it's not detected as in my PATH).
I tracked this GitHub issue and left a comment:
https://github.com/ublue-os/bazzite/issues/2132

The output of my journalctl is here:
-- Boot 921b5882663b4a7793c3bc8f826f5aac --
Nov 16 19:56:25 bazzite systemd[1]: brew-setup.service - Setup Brew was skipped because of a
n unmet condition check (ConditionPathExists=!/var/home/linuxbrew/.linuxbrew).
-- Boot c62517c75ad14564862337c1be40aa45 --
Nov 16 20:02:21 bazzite systemd[1]: brew-setup.service - Setup Brew was skipped because of a
n unmet condition check (ConditionPathExists=!/var/home/linuxbrew/.linuxbrew).
Nov 16 20:10:54 bazzite systemd[1]: brew-setup.service - Setup Brew was skipped because of a
n unmet condition check (ConditionPathExists=!/var/home/linuxbrew/.linuxbrew).
Nov 16 20:31:55 bazzite systemd[1]: brew-setup.service - Setup Brew was skipped because of a
n unmet condition check (ConditionPathExists=!/var/home/linuxbrew/.linuxbrew).


I even tried moving that directory to see if the output would be different:
Nov 16 20:33:16 bazzite systemd[1]: brew-setup.service - Setup Brew was skipped because of a
n unmet condition check (ConditionPathExists=!/etc/.linuxbrew).

Still more broken homebrew stuff.

When I run ujust update now, it's able to check brew and it says everything is fine. It does however correctly identify that my flatpak path is messed up and some my desktop isn't recognizing my flatpak apps. It says they should come back when I restart my session, but they're not coming back.

I'm having the same issue as the other guys on the GitHub issue and it was put in months ago and there hasn't been any movement on it. I'd really like to have my system working again. I would really appreciate any support.

Edit:
topgrade also fails:
Total size of inbound packages is 302 MiB. Need to download 302 MiB.
After this operation, 15 MiB extra will be used (install 1 GiB, remove 1 GiB).
Error: this bootc system is configured to be read-only. For more information, run `bootc --help`.
System update failed:
   0: Command failed: `/usr/bin/sudo /usr/bin/dnf upgrade`
   1: `/usr/bin/sudo` failed: exit status: 1

Location:
   src/steps/os/linux.rs:250
Retry? (y)es/(N)o/(s)hell/(q)uit

(it fails everytime I retry)
GitHub
Describe the bug Grabbed gnome-stable from bazzite.gg on 12 Jan CET and did a fresh install on bare metal from the bootable image. .linuxbrew/bin/brew was missing and ownerships were screwy. .linux...
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