Probably comes from しょい -> せい https://kobun.weblio.jp/content/%E6%89%80%E7%82%BA
Furigana placement on here is not necessarily correct/logical as they're algorithmically placed.
There's no reason to expect the furiagana placement here to perfectly correlate to individual kanji. It's just "the reading of the word place above the kanji for the word."
Furigana alignment on this version of jisho is still erroneous, as pointed out by Kim previously (and on jisho4).
These furigana issues have all generally been fixed on the beta version of jisho4:
https://four.jisho.org/search?keyword=%E6%89%80%E7%82%BA
On top of the fact that here, the kanji form is still displayed as a headword despite the [rK] tag, which has also been changed in the newer version.
As for せい, it indeed appears to be derived from そい「そゐ」 (or しょい), though the references I consulted don't fully bank on that.
角川古語大辞典: 「しよゐ」「そゐ」の転と考えられる。
日本国語大辞典: （「所為」の字音「しょい」の変化した語か）
ふりがなの位置、合ってるのでしょうか？
「せい」が、「所」の上にいる。「為」の上にはなにもないけど、それで正しい？
そもそも、なんで「所」なのに、「しょ」とか「ところ」ではなく、「せ」って読むの?