Why not positional variation?

[RadioFM]

Finally, the variants of the characters. In my opinion, the most important decision maker is the arc ‘)’.

Yes, it is possible the flourishes carry meaning.

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For me, the biggest problem with [n] being the final form of [i] is the existence of [ir]

Although the ir, iir and iiir endings could turn out to be somehow "equivalent" to their iiin counterparts, I feel they may be subject to different writing constraints. Specifically, we have a few instances of ir sequences occurring not at the end of word, but right before a iin sequence, with words such as dairin, ariin. Here are the few examples, in a dirty You are not allowed to view links. Register or Login to view..

Now, to be completely fair, the instances where this occurs are so few that of course, they may not even be worth considering in the grand scheme of the MS, and the fact that they occur in "LAAFU" line positions or consecutive folios, suggests they may be just exceptions found at the crossroads of different encoding mechanisms, or a coding quirk that was quickly dropped by the scribe(s).

But the fact that in the MS we have a bunch of matches for ri, the ones in You are not allowed to view links. Register or Login to view. even repeated in the same folio (so as to probably not be an isolated typo in that case), while at the same time having apparently no occurrence of ni whatsoever in the whole MS (You are not allowed to view links. Register or Login to view.), gives me the impression that there are at least different syntactic rules governing these different flourishes - maybe as small as the convention of "adding a whitespace / breaking the word whenever i is flourished as n instead of r ".

It's also worth pointing out that although very few in number, these ri matches are not unique to just one, but three different Lisa Fagin Davis' (LFD) Hands (hands 1, 2 and 3 per You are not allowed to view links. Register or Login to view., You are not allowed to view links. Register or Login to view., You are not allowed to view links. Register or Login to view.) - potentially implying that even in the face of having to write such a weird/rare word, these hands all agree that r, unlike n, can be followed by i .

There is also the phenomenon that some glyphs could easily be merged without much loss of information. Like you say, [y] and [a] is an option, but for example also [y] and [q].

Yes, that's actually an interesting idea. I guess in theory a verbose cipher could, for example, map a single letter 'a' to a combination of letter + whitespace + letter, such as " y q ", giving the false impression of a word break. By the way, does anybody happen to know of any previous research on possible "y q" substitutions, maybe trying to see if it fits the distribution of any letter or symbol in some of the candidate European languages?