Was Arthur Darvill ahead of the credits in season 1?
No, Victor Garber was first-billed from the start. Darvill may have been "big" in the UK, but he was fairly new to US TV.
Assuming IMDb's listing is in the correct order, the initial billing order was:
Victor Garber
Brandon Routh
Arthur Darvill
Caity Lotz
Franz Drameh
Ciara Renee
Falk Hentschel
Amy Pemberton
Dominic Purcell
Wentworth Miller
And I assume that means Purcell and Miller got the "with/and" prestige slots at the end, which are considered comparable to second billing, so that would make Pemberton the lowest-ranked regular due to being a voice role.
The initial second-season order had the same first five, followed by Matt Letscher and Maisie Richardson-Sellers, then Pemberton, with Zano and Purcell in the final prestige slots. The current order is Routh, Lotz, Richardson-Sellers, Pemberton, Tala Ashe, Keiynan Lonsdale, Zano, and Purcell. So the veteran cast members are still in their original relative positions, allowing for departures, with newer cast members in the order of seniority. Evidently Pemberton's seniority or her occasional on-camera appearances have given her a boost in the ranking, with Ashe and Lonsdale as the newcomers. (And it illustrates how much the cast has changed. Only 4 of the original 10 leads are still around, 5 if you count Darvill.)
So even though Sara is the clear lead character now, the only way she'd get top billing is if Routh left. It's very rare for two cast members' positions relative to each other in the credits to change; if one is above the other, they'll stay above the other. And usually the newer cast members get lower billing. Although there have been cases where a lead actor has been replaced by another lead actor who got top billing above the longer-standing veterans, like Earth: Final Conflict and Stargate SG-1. (Both of which were cases where the show brought in a new male lead rather than just promoting the female lead to a starring role she was more than suited for. Typical.)