That’s probably an I/O issue. I’ve had this problem when my BTRFS mount options were misconfigured. Also happened to ext4, but that couldn’t do snapshots before apt operations so it didn’t really need to lock the FS as much.
You can try reducing the I/O priority of intensive processes and filesystems and double check your mount options. If they’re optimised for HDDs, your SSD performance may suffer.
In my experience, Windows does a lot better when the system is overloaded with I/O or runs out of RAM out of the box. You can tweak most of those options out of the way, if you know where to look.
Specifically for BTRFS, fsync operations are quite intensive. You can use tools like eatmydata to reduce the impact by temporarily disabling fsync for a specific command (may not work with PackageKit software). Tweaking the BTRFS layout to exclude directories like /var/log and /var/run can also help reduce the impact of things like snapshots and deduplicated operations.