I would cut it a little slack if the pictures were taken by your buddy who went to go see it. If you rushed to clean to the boat every time a looker came to kick the tires, you would go crazy.
You cannot tell anythign about the quality of the transom job by those pictures, you need to know what materials were used, who did the work, and pictures of the re-build. Anyone re-building should take MANY pictures so you can document the quality of the work !
Also, just becasue the hatches are rough does not mean anything other than the hatches are rough. For a pure fishing boat, I personally would not go much nicer. For a fishing boat where functionality is of first concern, I would actually just slap a few pre-made hatches on there.
fuel/water separator needs hose clamps.
One thing you did not mention is that tank, ask if its original and if it was moved/replaced?
I do not know about the drainage, you need to talk to the guy who rebuilt it. Who ever it was did a pretty good job on the enclosure, the edges are fair and it blends into the sole pretty well. Its not a bad job from what I can tell by the pictures - which is not much
Talk to the guy yourself, get the full scoop from him, and ask for pictures of the rebuild!