Tool use is an ability check, but it is not a skill check. So, per LotRR, it is not subject to having a Blessing Die (which requires a skill check).
But a skill check is an ability check, so I see no reason to deny a Marvellous Artefact Tool Set that would add a Blessing Die to ability checks using that tool set.
The reasoning behind only MA and not WI, is that a tool set has its own proficiency and doesn't encompass uses of other tool sets. For example, smith's tools are for smith work, not cartography, or woodcarving tools are for woodwork, not jewel making.
I suppose (though it would be quite a stretch) that you could have Smith's Tools of some skill, say medicine, that would give a Blessing Die to smith tool use and medicine checks. That would be an odd combo, and I don't see any skill that would be a good combo with any tool set. Maybe Persuasion with calligrapher's supplies when writing a letter, though just Persuasion would suffice, both are not needed.
Therefore, I house rule, Marvellous Artefact tool sets, but only for that tool set proficiency. Your mileage may vary.