I think Buildcraft is included for the sake of Thermal Expansion, Forestry, and Railcraft as they rely on Buildcraft a great deal. It's probably more of a matter of most of the other mods relying on the one. That said, have you seen refineries? They refine oil in those tiny blocks by hovering rectangular prisms around it that glow at it. That's either black magic or voodoo. Not to mention it transfers kinetic power around its networks via little blue corner turning lasers.
I don't think anyone will deny that Forestry goes significantly beyond science. It uses a rainmaker machine, and many people have described its farms and harvesters as "magic blocks." Forestry's automation probably cannot work without Buildcraft pipes to direct everything where it needs to go.
Redstone seems rather magical. It was the first feature (and then later pistons) to allow for any kind of mechanisms, automation, or hint of industry, but the source of the energy is... hard to deny as magical. Thermal Expanion's machines can do some pretty "magical" things already, but throw the Redstone Conduits and Energy Storage Cell into the mix and it really loses the feel of science. It's because almost half of Redpower (it's even in the name) is focused around the compact circuits and enhancing Redstone that I'll be a little surprised if it doesn't make it into the Magic World pack too. So basically I'm blaming Redstone here, but I'm not at all sad that Thermal Expansion gives Magic World a lot of what it would otherwise lack. So far the only alternative for ore processing and yield increase in this pack is the Infernal Furnace, which does not achieve 200% yields at all. That would improve if Factorization were included, but so far Thermal Expansion and Redpower are the only mods I've seen that can have buckets automatically filled somehow for something other than a Crucible, which means no Factorization factory is really complete without Thermal Expansion (or Redpower) handling the buckets.
Railcraft uses the magic of Enderpearls to teleport passengers on, has rails that magically link carts together, mess with momentum in all sorts of ways, and the High Speed Rails apparently run on the power of Blaze Rods. It has an industrial feel to it, yes, but many of its components manage to feel quite mystical. On a more practical note, Railcraft seems to me to be one of the most reliable distant transportation options for you, items, fluids, etc. Mystcraft works too, but not completely without Railcraft accompanying it. Not to mention it's the mod that adds World Anchors. Restricting it from one of the packs would be just not fair.
Steve's Carts' assembly block has nothing science-y about it, at least not in its current incarnation. It also has invisiblity somehow using an Eye of Ender, invincibility, and uses galgadorian metal which clearly has magical connotations. Steve's Carts is one of those mods that feels like it's in limbo between science-y and magicky.
Golems are Thaumcraft's transportation system, but so far they still fall behind in usefulness for several tasks. You could make an underground golem tunnel to rely items across distances, but that's bound to be more resource intensive (both game resources and your computer) than either Buildcraft pipes or Railcraft carts, and slower than both as well. Thaumcraft's solution for long-distance item transportation, so far, is to add more golems and more chests compared to more pipes with an occasional gold pipe and with more rails, possibly high speed rails. No matter what the method, golems included, World Anchors will be needed. I don't think golems can see through Mystcraft portals either, so unlike for Railcraft, Mystcraft portals are not a solution. Sorting systems are even worse. You can sort with golems, but you're basically going to have to make a large convoluted room full of chests and stone golems and a web of indicator blocks. It's doable, but it just can't compare to a line of Item Unloaders or, even better (usually), Diamond Pipes. Even if you refuse to see any magic in the other mods, they at the very least help fill in the gaps and let you accomplish the things that Thaumcraft doesn't (yet at least) manage to do.
Meanwhile IC2 goes out of its way to avoid claims of magic, even fluffing it so that lapis lazuli is somehow highly conductive.
I'm far more curious/confused as to why Factorization is not included. Half the mod is undeniably magical, from the Wrath Igniter onward.
