Well on a 24 hour system, midnight is 0, right? They start counting at 0, so its not surprising that they would apply the same logic to when you start counting over for the pm. Personally it makes a whole lot more sense to me than starting the PM with 12 and then going back to 1, 2, 3. My guess would be the original use was for the 24 hour system and it just kinda got extended over, but that’s pure speculation.
Also I checked some books I’ve read and couldn’t find it being used for noon, but I did find 午前零時 which would imply that noon is a potential use in standard japanese or else they probably (?) Wouldn’t have bothered to include the 午前.
Its also worth noting that ０時 is only midnight though iirc.
EDIT: Got a source on my last claim because I wanted to make sure I wasn’t passing along wrong info
そのため、 昼の12時を指す表現は午前12時のみであり、午後0時という表現は法的には存在しません 。
So yeah its supposed to only be midnight, but I think due to 零時, its possible someone might mistake it for noon despite not being technically correct. Like I can find where 午後０時 is used on the internet to mean noon, but ０時 is always midnight. Which makes sense. The reason I’m seeing online for using 0時 or 零時 when talking about noon is that its just a lot easier to understand and less likely to be misinterpreted when it follows either 午後 or 午前.