I think you missed my point. This is IndustrialCraft. Key word there: Industrial. To me, that means this is a primarily an engineering expansion mod. This is not ResearchCraft or ScienceCraft or BiologyCraft or some other variant. It is supposed to make Minecraft feel more like an Industrial environment. Not a research lab. Not a science project. An Industry. Industries take already well known science and applies them to the limit. It takes well researched fields and furthers them for profit. It does NOT explore entirely new fields of research for "why the hell not."
Crops are present in Industrial Craft to enhance gaming experience and to add closely related elements to the game, so I don't see why this is so horrible decision. Industry and research are not the same, but there is great connection between the two and many IRL organisations cover both of them.
Think about lategame scenario: You are standing in your large base, where everything takes care of itself, energy is produced constantly without interfering. Now it's the right time to research, so you can later integrate the results of your research into your big automated factory. Currently there is now way of automating plant harvesting/fertilizing, BUT this is only beginning. It is too soon to say that whole concept is very wrong and does not even fit the game.
Furthermore, I want to hear your logic as to why you chose to put an Iron Ore block under a random growing plant. What keyed you into Iron Ore instead of one of the other couple hundred blocks you chose? Until I can get a logical explanation for why you chose Iron, I'm not going to accept your anecdote as justification for this system (and for that matter, nor do I believe you got absolutely no help from source or someone in the know to come to that conclusion ... there I'll say it). Or maybe you're just crazy and decided to try all the combinations of 100 or so valid blocks in the 17 potential logical locations and somehow have compressed 10^36 growth trials into the span of a month?
There was actually clue about every plant so far. Seeds of ferru were analyzed and keywords for this plant were found (Grey stem, Metal). Once i saw them, i knew this plant is going to produce something iron/tin related. Someone noticed, that Ferru cannot reach its final stage, so I looked into plant suggestion thread to find my earlier suggestion (this one), to see if there are any similarities. Then I suggested the person who discovered it adding Iron ore under soil block. I was just a guess, but it worked. My reasoning behind putting iron ore under soil block was simple - soil around iron contains greater amounts of it, and Rusty root (as i named it) had ability to absorb iron and create a thin layer of it all around the plant, to protect itself (since it cannot process iron). Iron ore is not required for plant to grow, but is required to provide enough iron particles for the plant to reach stage, where it's covered in iron.
Same applied to aurelia.
Redwheat is different, as I am still not aware of any conditions needed to succesfully harvest the plant. However, it is also based on suggestion (here), so everyone is free to try.