These spelling options are a work in progress, but are provided in the hope that they will help performers around the world find a system that they are comfortable and familiar with, especially those who are native speakers and readers of Portuguese and Galician, as well as other modern Romance languages such as Castilian Spanish, Catalan, Italian and French. If you don't fit that description and cannot immediately see the benefit of having alternative spellings, don't worry: you won't miss anything by ignoring them. Stick with the default settings and you'll be getting exactly the same information as you would from the others, just with a slightly different veneer.
I would like to emphasize—just in case it is not completely obvious—that these variant spellings have nothing to do with translations into the associated modern languages. Nor do they represent variant pronunciations: whether we write ben or bem, the pronunciation is exactly the same, i.e. [bẽŋ] (and indeed the pronunciations [ben] and [bem] are equally wrong). More generally, the availability of a Portuguese-based orthography is absolutely not intended to encourage an overtly modern Portuguese pronunciation of the Cantigas; everything in the Pronunciation guide still applies.
As well as the main lyric texts and the underlay to the music, my footnotes also use the variable spellings where it makes sense to do so. However, when talking about the specific form of words in a specific manuscript, I do of course keep to the original spellings.