Thanks for the feedback. After starting classic Daggerfall again this morning to re-check with my Mister50 character (50 in all spell skills), classic is now producing Water Breathing results matching the spreadsheet. Earlier the values were very different for Water Breathing in classic.
This is the second time this has happened. The first time, I just assumed I had made a mistake. I triple-checked everything this time and classic was definitely outputting different values for the same character with the same skills on the same effect at the spellmaker.
I think I might be falling afoul of is an unusual bug in classic where it's messing up costs in the spellmaker. Next time this happens, I'll restart the game before I assume the spreadsheet is wrong.