Enviei a questão para a Mind Clash e esta foi a resposta que eles me enviaram:
Dear Renan,
Thank you for reaching out again! I'll copy my reply below, it could not be delivered before.
Ironically, what you describe is exactly the problem itself - the fact that Shard stacking would unlock TWO very powerful effects at once would make building up Shards instead of spending them an absolutely dominant strategy, which is not our intention. Also, certain Contraption effects and Magician powers could make absolutely overpowered combos, which would exacerbate the luck of the draw that is already present with the Magician Powers to an extent. I'm not saying that the combination of the two expansions couldn't be house ruled an played (the UI definitely supports it), but would almost certainly be a quite imbalanced and arguably unfair experience.
While we didn't really experiment with this combination for a long time, there is a thread on BGG where someone claims they regularly play this combination - maybe they would be able to help you with the specific house rules they apply. 
I hope this information helps, please let me know if any other questions come up!
Kind regards,
Tünde