Huh. Someone posted that exact sentence on HiNative quite recently. I didn’t know what to make of it then, either. =P Kinda wish I’d hung around to see if any native speakers replied, but it’s been well-buried by now. Wonder if there’s a search function.
The fact that it’s followed by かしこまりました suggests to me that it’s a standard phrase spoken by shop-people. Googling suggests さようでございます might be the respectful-polite form of そうです, but aside from the fact that さよう is a word (and it’s not さ on its own), it’s so specific and archaic that it’s gotta be a bad example sentence. There’s no way that version of さ can possibly rank in the top eighty most common words.
Anyway, that さよう is 左様, which is supposedly the origin of the farewell さようなら. However, the kanji 左 sitting on its own means “left”, and would be more typically read as ひだり (though it can be read as さ).
I wonder if this さ is actually supposed to be the suffix -さ, which means “-ness”. As in, 大きさ = size (= “bigness”). Or 差 = difference. Surely Koichi would have checked that the example sentences are correct, though. Maybe we need to e-mail him and ask. Or Mami…
http://howtojaponese.com/2010/10/14/power-up-your-sou-sayou-de-gozaimasu/