Is [a] always [a]?

[-JKP-]

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This said, your idea of treating aiin as a single entity makes perfect sense: if the writing system is phonetical (meaningful or not) iin could be like an accent, that in a few languages (e.g. Italian) is only used for vowels at the end of words.
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Marco, thanks for the graph. Data visualization is always appreciated.

Your comment made me wonder... Have we ever compiled a list of possible interpretations for "ain"?

• I know that many people have suggested "and" mainly because it is such a common glyph sequence and maybe also because it begins with the "a" shape + minims ("n"?) plus a glyph that sometimes looks like a "d" but it seems to me quite a few of them were suggesting "daiin" and not "aiin" might be "and" and that seems less likely to me. I think it's important to make a distinction between "daiin" and "aiin".
  

But to get back the various possibilities, in addition to the one you noted...

• Another possibility is a grammatical ending (like an ending that creates a noun or adjective). It seems too frequent to be the ending on a specific word but if it were something that could modify numerous words maybe that could account for the frequency.
  

• One possibility I may have mentioned on my blog when I was talking about Roman numerals, is that perhaps it's a value. What comes to mind (just as an example) is the way medieval texts classified various things according to their elemental properties. For example, it might be hot in the 3rd degree or cold in the 2nd degree. There are instances of av, aiv, aiiv, and aiiiv (I use "v" rather than "n" in my transcripts because it looks more like the tail that occurs on the VMS chars). In other words, potential values from 1 to 4. In this scenario, I'm not sure why the "a" would be there. If it were hot/cold/wet/dry in 1 to 4 degrees (grado) then one might expect the "a" shape to have 4 variations but I'm not sure it has 4 consistently-discernible variations. Or, if the "a" is actually a curve followed by a ligatured minim, then potentially it's 1 to 5. If it is numerals, maybe it's not elements, maybe it's numbers for something else.
  It's only one idea, not necessarily the right one, but the concept is that maybe the minims indicate values... for something. The "c" shapes only go up to 4, but if the minims are maxed out at 4, then the two groups would have the same max.
  
• Maybe it's a connector or stop-point. If so, it's a horribly verbose one, but we don't know what's going on in the VMS, so I thought I'd add it to the list.
  

Koen's examples are moderately variable, especially considering they were sampled on the same folio. It's very hard to say if the variations are meaningful.

I had some other ideas for what ain could signify but I don't want to make the post too long and I'm sure others have ideas too.