What watchdog do you mean? I've ssh'd into my Mazda3 and was planning on doing it again soon, but I don't know what you mean by that.
If you don't disable watchdog then when it starts up and isn't working watchdog will have it automatically reboot. Since this isn't a transient issue, but a misconfigured file it'll just keep rebooting making it very difficult to ssh back in and fix the file.
If watchdog is disabled then while the infotainment system won't work it's easy to ssh back in and fix the file.