Sorry for the horrible thread necro, but I found it on a related Google search, so I figure the info might as well be placed here for future searchers.
The basics of the "forbidden" EMC generators are those that abuse exploits and/or are very low effort for disproportionately high reward. The Flax Capacitor is too easy to automate for the frankly absurd EMC it generates (you have no need to replant the crop, and flax is one of the more dense EMC crops even if you only break a single block). The Dark Room takes advantage of something that was fixed as a bug in later versions of MC (Fairly soon after 1.2 from what I recall). If you try in a modern version of MC (even 1.6.4, let alone 1.7.10) bonemeal won't grow grass/flowers in pitch dark. The milk/stew generators have gone back and forth... it's more a commentary on Xeno's choice of values for the fluids milk and mushroom stew and just how relatively high they are for the speed and ease at which you can generate them. Personally seeing as how there STILL isn't a cooldown on milking cows and mooshrooms? I *personally* say this one is legit. Not official stance in any way. Cross mod interaction exploits like macerating blaze rods should obviously also be forbidden, as should item duplication glitches (there was one insane EMC generator that duplicated powered rails... it scared me).
It should be possible to create something similar to the flax capacitor with more blocks/space using normal crops. Block Breaker and Deployer (I'm a bit ashamed at how long it took me to come up with that, I actually had to go find a list of the RP2 machines to remember which block it was :-( It's been a while since I've played with RP2) which would be legit. A deployer for seeds, a deployer for bonemeal, and a block breaker to break. There should be enough sides left for redstone control and item transport.
But honestly? Just use a highly efficient mob tower with auto-kill drop trap. It's 100% legit (anyone that says otherwise is being a complete and utter derp. It's 100% vanilla mechanics, or well would be if a decent item transport (hoppers) had existed back in 1.2.5).