Here are the reasons for the feature working the way it does:

1) SBSettings and the SBSettings toggles are separate apps. SBSettings cannot configure the toggles without a significant amount of work which will not be done anytime soon. Therefore defaults for each toggle must be used.

2) No one should be rebooting their device very often. I reboot mine maybe once a week. So the SSH coming on when I don’t want it is very seldom.

#3 is a bit longer. But in short, you want SSH on reboot. If your device is hosed for whatever reason, this is likely the only way to fix it without a full restore. It is a protection mechanism for you.

During the boot up, there is a long period during the apple logo where the device connects to the network and you can SSH in. That’s the main window of protection. Here are some examples:

Example #1:
Lets say you installed Intelliscreen and now your device won’t boot (this is a paste real-world example).  You just get apple logo and then it reboots. It doesn’t use mobile substrate so there’s no safe mode. Instead, it reboots over and over.  During the apple logo you can SSH in (for about 2 minutes and then you’re cut off). Here you can do a few things:

1) apt-get remove com.intelliborn.intelliscreen  <– uninstalls intelliscreen
2) If you know where the files are, you can manually delete them.

The device boots! (Note: I used Intelliscreen but it could be something else)

Example #2:
Another example, your springboard plist is totally corrupted and the result is the same. Apple logo and infinite reboot. Via SSH you can remove /var/mobile/Library/Preferences/com.apple.springboard.plist

Example #3:
Lets say you don’t know what’s wrong. In SSH you could tail -f /var/log/syslog (or enable syslog and enable it) and get some hints. The possibilities are really limitless.

In short, SSH on reboot prevents you from having to restore your device in critical error. If you don’t like it, as soon as your device boots up, disable SSH.

On another note, the SSH daemon is extremely low power and low overhead. It does not use any battery if there are no SSH sessions connected. Personally, I don’t even disable SSH. I like it always running. If you’re paranoid, change your root password.