That's an interesting point.
I can see advantages for both approaches. The advantage of the current approach in terms of the early game is more energy for research, automatic replacement of fungus by growing forests, and the creation of defensive terrain around the AI's bases (forests both slow incoming rover attackers, most notably probes, as well as provide a defensive bonus to units in the area). In terms of the middle game of course the AI will benefit much more from Tree Farms, since if they built mines/farms everywhere in the early game, they won't tend to replace those with forests later when it makes sense to do so.
The mine/farm approach would help momentum AIs more in the early game. I guess you are seeing a personal bias here, as I tend to play on huge maps and like to see conflict later in the game rather than earlier, with higher tech and larger empires. To keep a game interesting I have been known to give the AIs all my tech when they have large, but low-tech, empires late in the game, thus guaranteeing myself an entertaining war of massive proportions.
