The builder seems to call Block#getMetaFromState directly instead of invoking Block#createStackedBlock when creating ItemStacks for silk touched blocks.
The vanilla silk touch logic will also invoke Block#createStackedBlock, as can be seen in Block#harvestBlock.
The problem is that this can set a non-zero metavalue to the ItemStack, even if this is not intended by the block.

This causes issues like CyclopsMC/EvilCraft#515, and possibly also for other blocks like vanilla Redstone when it is activated.

I'll check it out

I cannot call createStackedBlock() as that is not a public method. Any other proposed solution?

Ah, my bad, didn't look good enough at the method signature...

Reflection of an AT would be a straightforward, but not that clean solution.
Unless Forge would add a default AT for making that method public.

Alternatively, you could call harvestBlock with a fake player holding a dummy stack that has the silk touch enchantment. The only problem is that this drops the item entity in the world, so you'd have to somehow detect and grab this...