namely:
"MANASTEEL": "botania:manaResource 0 1",
"B_ELEMENTIUM": "botania:manaResource 7 1",
"TERRASTEEL": "botania:manaResource 4 1",
"darkSteel": "enderio:itemAlloy 6 1"

they do not add recipe as they should(must add them manually with Crafttweaker, but I don't know if I can repair the lumberaxe then)

You put them in materials.json from D3Core right? (the title sais Material.json, missing the s). I wanna rule that out before I start digging 😄

Edit: Would you mind testing to see if they are repairable, and post a full log?

sorry for the title typo, here is my whole file, with txt appended to ext for upload
materials.json.txt

edit: i'll try that when MC opens

nop, Manasteel not repairable
log line containing manasteel:
http://pastebin.com/5QQ4LYrn

after a couple of test, it seems like only BaseMetal ingot can repair Copper and Steel, even if I have 6 source of each(mot much of a problem as I normalize to BM, but still)

Its possible that this is one of the limitations on repair materials and meta data.
Minecraft is weird. It doesn't properly support metadata based repair materials in all scenarios.

After more testing, ManaSteel is not repairable in the Anvil, but is still fusionnable with another lumberaxe, as are all

that makes sense as they are the only one with metadata != 0
if possible, a good workaround for that would be using oreDict, but I think that's limited too

There is no way to use the oredict here.
Original MC uses an Item (not a stack) so no metadata, Forge already added the ItemStack (but then doesn't seem to fix all of the bare item uses). Making it oreDict would break that even further.
Since most people use Minetweaker, I decided not to add more hacks to do that.

only other way would be to hard code compatibility, or mark them as "must use CraftTweaker and repair by crafting"

You can't even really hardcode it, unless I basically add mini-minetweaker by adding recipe sync across server - client. (Since the server can have materials set/not set that the client doesn't, thus adding/removing recipes). I could add a warning about all of this to the log.

I think just a mention in README.md could be enough, trying to limit log size lol
Other than those technicallity, I think we can close this, as it is a Vanilla Limitation™
onward to # 13 then :D

yea, I don't like log spam either. I'll make it sum up the elements in one line.