Orchards of fruit/nut trees are both commercial agriculture, and centered around perennials. Are industrial orchards less productive than industrial farms?
Thinking about the cost per calorie of apples versus oats, to pick an example that works for me, I would say the answer is very much yes. And ultimately, from the plant's perspective productivity should be a question of efficiently storing energy.
The limit there is likely that no one has figured out how to make an annual fruit or nut tree.