If resource cost is an issue the largest size you can afford is the most efficient, because space and seeds cost virtually nothing compared to additional machines and upgrades. If it's enabled the "villager vacation portal" makes top-tier upgrades super easy, including those for Storage Drawers to use as barrel replacements. There's no real issue with huge crop farms except for the loss of per-tile production efficiency, but with large treefarms you lose out on saplings. The "maximum recommended size" will depend on the tree type though, especially if you allow 2x2 spruce/jungle ones to grow- The MFR machines only ever process one block at a time, so those giant trees take ages to cut down.
If resources aren't an issue you can get insane production speeds with the minimum 3x3 size. Place the Blood Magic ritual underneath it and sprinklers etc. around the sides/above it, then overlap multiple harvesters if necessary. This does not work for Acacia-style trees because they need an additional block clearance to the side to grow, and AgriCraft crops need an air block directly above them so put your sprinkler one block higher. Once you stack several growth speed buffs the harvester can't really keep up with sizes larger than the basic 3x3. As AgriCraft crops don't have to be replanted the minimum farm size for this design is 5x5x5, +1 on the height if you want a switch for the ritual. As the outer ring only contains harvesters and sprinklers you can overlap adjacent cells if you use EnderIO conduits to compact the piping.
I don't know of any "perfect" replacements other than the three soy/tofu variants replacing all animal products, and if your goal really is to have access to all food items you probably should include all crops as well, for completeness' sake.
Now, as for actual practical uses, the culinary generator scales its RF/t as 4x the hunger value of the food (FTB Infinity 2.4.2 default config, no Expert mode) and the highest yield you actually get with vanilla cake at 64RF/t. Pam's has very little variety in the actual stats of the food, your top-tier options are Beef Wellington, Beet Burger, Delighted Meal, Epic Bacon, Hearty Breakfast, Meat Feast Pizza and Sausage in Bread. As the burn time/total RF yield scales with saturation the Pam foods are better than cake in that regard (while yielding 3.5RF/t less). The easiest for autocrafting are cake, Beef Wellington and Epic Bacon.
Another option is to run wheat through a SAG Mill followed by two TE furnaces with the food upgrade, which produces 12 Pam's Toast per wheat on average. A single output furnace can fuel dozens of 64x culinary generators, but the setup cost is huge due to the low RF/t yield of Toast.
The Gourmaryllis has an additional quirk: its internal buffer is smaller than the mana yield of a full 20 hunger points. In fact the cap is reached with about 10 points, which corresponds to about 40 RF/t in a culinary generator (search for "rf" in NEI while you have the UI of the generator open, this displays all foods with their corresponding yield). The most practical food I found was the Cucumber Salad, which for some reason is almost as nourishing as a large burger or chicken dinner while containing only a couple vegetables. It doesn't even require soy/tofu, so you're not bottlenecked by slow-as-molasses Pressers either.
As for vertical farm designs, I tend to avoid them. Half of the farm (the planter+sludge boiler+pipes) looks ugly and the ritual is best hidden underground too. Also it's much easier to survey and diagnose problems when you can walk/fly over a large area and look at the crops. That said, the ritual cell could make for a nice futuristic "food synthesiser".
