Yagroot Roots are assigned the leaves tag, even though vanilla's mangrove roots are not. (Which seem like the closest parallel)
This means the roots instamine with shears, which mangrove's don't, with a tool made from non-Aether materials.
Could be a design decision w.r.t. mods that chop trees from a single block (and those probably only checking for mangrove roots specifically), but seems like an oversight.

Thank you for reporting it anyways, but for now it is a choice we decided to stick with.
Still I won't close the issue yet as we don't really know if there will be many negative implications with it, so we might change that in the future.