Thanks for pointing out the Wat issue. I've moved the extra scientist slot to the Research Lab in the current development version.
I agree about the watermill, I've been considering buffing it. In early game I've found the watermill useful for my military city once all hills are being worked. It's a good production boost when you've run out of other sources.
The main bonus of the engineer slot however is if you're running with a specialist economy, such as if you're playing the Ottomans (which have +33%

creation as a new trait). It's converting 2

into 2

1

3

(science from the buffed Landed Elite policy in the tradition tree) which is quite good, especially since the Manufactory improvement got a buff in
Terrain Improvements. In the renaissance with specialist policies it becomes insane, up to +0.4

1

3

3

3

.
Basically, it scales better as the game goes on. To improve its early game value, someone suggested adding a 2

to the building itself, which is an interesting idea.
In most of my games I build the Smokehouse if I have two of the resources nearby. That's 4

for a 1

/turn maintenance, quite good. It's situational, but still useful. It'll be better once we can convert the Maritime bonus from fixed food to a % increase.
You're right that Siam gets a bonus, I haven't seen the civ listed at the top of any "most powerful civ" polls however, so I felt the buff makes sense. Post-renaissance they have 3

from Maritime compared to other civs' 2

, so it's 50% in mid to late game. This is the period Maritime makes the most difference, when empires are larger.