Sorry. The upper drain is definitely incase water splashes into the rear were the fuel tank and battery go. It's also sunken in there. About 6 inches.
I commented on this with a like but I'm having a concern. There are several types of "splash wells" that catch the back wash that sometimes comes over the transom, especially 15" transoms either from rough water following seas, or by the boat being operated at reasonable to high speed and the operator chops the throttle abruptly causing the transom the sink and back wash...the water the boat was pushing out of the way no longer has anything holding it back and it moves forward toward and into the transom splashing over it.
Another drain type device is where the deck is flat till you get in the general area of the transom and then falls down...with width of the deck stringers to a lower leves glassed in area......your comment about the location of the battery and fuel tanks made me thing of this.
On some of these configurations, if you get on your hands and knees with your head against the inside of the transom, looking back at the step from the main part of the deck to this lower part at the transom there will be round drain holes in the sides of this area where I have seen a thermosbottle type lever action removable plug was inserted in usually 2 holes, one on either side of the step. That would be the flotation air pocket. Looking at the transom just above this lowered area ....the surface upon which the fuel tank and battery are resting would be the deck drain. The lower hole would then be a bilge drain that drains out any accumulated water sitting between the outer hull and interior deck.
Splash wells are usually shallow depth, enough room to get the transom engines clamp brackets above the bottom and deep enough for the engine tilted up in the transom bracket extended position, allowing room for remote control cables to make a bend without kinking...usually requiring the powerhead to be tilted to one side when raising to have enough room for the cables to curve without binding.
A combination splash well as described here plus the lowered area at the transom of the deck where the battery and tank are mounted were sometimes used by boat builders.
So what does all this mean to you??????? I don't know. You asked about holes and these are some examples of things I have had and seen over the years along the lines of the subject matter. Hope this Helps.
Mark