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In short - if I have a Synesthesia scroll in my hand as an arcane caster with Unified Theory do I use a legendary proficiency to see if I can cast the scroll?
Your question is a bit unclear.
First, the Unified Theory feat is clear:
"Whenever you use an action or a skill feat that requires a Nature, Occultism, or Religion check, depending on the magic tradition, you can use Arcana instead."
Of course, if you are making an Arcana skill check, then you use your Arcana as normal (which should be Legendary proficiency as that is a prerequisite for the feat).
BUT, if the spell in question is on your spell list, then you can cast it without a skill check. You use your normal spellcasting proficiency (not your proficiency in Arcana).
So, I assume you are asking if you can use Trick Magic Item to cast a spell NOT on your spell list (i.e. from another tradition, like Synesthesia, which is an Occult only spell) as that requires a skill check for the tradition of the magic item/spell in question? In that case, yes, Unified Theory lets you use your Arcana skill to trick the item.
Note, if you do NOT have Trick Magic Item, then Unified Theory doesn't let you cast from a scroll with a spell that is not on your spell list. Synesthesia is Occult - so you need to use Trick Magic Item.