When you have separate btrfs subvolumes for /gnu and /var/guix, you'll
encounter this error running `guix system init /mnt/etc/config.scm /mnt`
when it tries to copy things to /mnt. My guess is that guix is trying to
remove one of them but fails as they're mounted.

I encountered this issue while I tried installing guix system on my main
laptop. But I have encountered this before [1]. When I installed guix
system on my secondary laptop. I worked around it back then by using
guix-0.15.0.

For my secondary laptop I have this layout
| subvol                | Mountpoint | Comment         |
|-----------------------+------------+-----------------|
| __current/guixsd-root | /          | root for GuixSD |
| __current/grub        | /boot/grub | grub config     |
| __current/guix        | /var/guix  | guix stuff      |
| __current/gnu         | /gnu       | Store etc       |
| __current/home        | /home      | home partition  |

For my main laptop I tried:
| subvol | Mountpoint | Comment        |
|--------+------------+----------------|
| @      | /          | root for Guix  |
| @grub  | /boot/grub | grub config    |
| @guix  | /var/guix  | guix stuff     |
| @gnu   | /gnu       | Store etc      |
| @home  | /home      | home partition |

Found another thread that also had this issue [2], and the same
workaround worked for me. I.e. simplified the layout:
| subvol    | Mountpoint | Comment        |
|-----------+------------+----------------|
| @         | /          | root for Guix  |
| @home     | /home      | home partition |

This seems to just be an issue when running guix system init, as I've
been using my secondary laptop with separate subvolumes for /gnu and
/var/guix without any issues since 0.15.

The guix version I used to install my main laptop with was
1.1.0-25.44c6e6f. I generated it with

  guix system disk-image --file-system-type=iso9660 \
       gnu/system/install.scm

As described in the manual.

Thanks

[1] https://lists.gnu.org/archive/html/help-guix/2018-12/msg00055.html
[2] https://lists.gnu.org/archive/html/help-guix/2019-06/msg00259.html