When Transform is involved, most species-specific items (including Eviolite) apply based on the original user's pre-Transform identity, except that in the case of Quick Powder and Metal Powder (the ones that are specific to Ditto, and thus the only ones likely to interact with Transform in a battle where move legality is respected), as well as all Z-crystals, the item checks the post-Transform identity to determine if it can apply. For example, if a Ditto transforms into a Pikachu with Volt Tackle, Ditto will not get to benefit from Light Ball (original source is not Pikachu), nor Quick Powder or Metal Powder (because those items care about the target, and the target is not Ditto). However, if it's holding Pikanium Z, it does get to benefit from that, and use a one-time Catastropika.
If a Mewtwo somehow transformed into Venusaur, holding Venusaurite would not allow Mewtwo to mega evolve afterwards, but its own native Mewtwonite mega stones would, in which case it would keep its transformed moveset, but revert to the regular stats of whichever Mega Mewtwo it has the stone for. In addition, it would lose its Grass/Poison typing in favor of either pure Psychic or Psychic/Fighting.