Iron - Obviously
Tin/Copper - Well no, it can't. It would auto-alloy them if it did anyway, making it useless.
Gold - Have you SEEN the agrarian skies nether? Are you seriously contemplating locking gold behind that... *shudder*
Silver - Actually with witchery in 1.7 you can... oh that takes ore, nuts. There are a few mobs that deal with silver... not many though. You might be able to make it a byproduct of processing blizz powder like you can get redstone/glowstone from blaze (apparently).
Diamond you would seriously want to be armor which I'm relatively sure a smeltery could be made to melt down into diamonds and cast into the gems, and with AgSkies Emeralds are obtainable via villager auto-spawning and melting.
Thaumic Transmutation CAN be automated, but there are no nickel, platinum, or aluminum transmutations.
Nickel is also core to much of the AgSkies experience, as are platinum and even aluminum (mostly because of the 5 quests that involve Mariculture... I still say that mod doesn't fit). Invar is used EVERYWHERE, and platinum is needed for enderium.
If you're going to minetweak the TE metals away, then you're not really playing AgSkies anymore. Definitely a modded skyblock, but not AgSkies.
Aaand I never hit "Post" on this. I feel smart... yes that is totally not the opposite of what I was feeling at all! <Sarcasm mode deactivate>
Edit:
Honestly MCF needs to give original posters basic admin capability in their own threads and have the sectional and global moderators back the hell off.
ESPECIALLY because their rules are... draconian. Basically anything is against the rules and they're within their rights to fucking BAN you for nearly anything and the moderators decision won't be overturned and they won't be punished even if it's well outside reason and stated policy. I love Curse as a distribution platform, despite the shit the pull on the WoW client (which is my only other experience with them as a distribution platform). But their forum handling is some of the shoddiest I've EVER seen. I didn't know it was possible to screw up this badly without intentional malice.