I find the second option, where in/iin/iiin are different characters, more plausible because it would likely increase the character entropy, whereas an equivalence between 'i' and 'n' would decrease it even further.
The 'iin' stroke seems to occur occasionally in manuscripts of the time (it's not rare), and can indicate an abbreviation.
The following are some examples from Cappelli.
'iin' as a 'u' in 'anuu', encoding 'annuum':
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'iin' as a 'u' in 'qartu', encoding 'quartum':
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'in' as an 'i' in 'fli', encoding 'falsi':
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'in' an an 'i' in 'sait', encoding 'sanitatis':
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The 'n' stroke also occurs as extension to 'a'. Here it is in 'spear', encoding 'specialiter':
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In 'subaliu', encoding 'substantialium', the 'n' stroke occurs twice:
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The result can be a complex mix where:
'i' takes the form of EVA 'i' or 'in'
'u' takes the form of EVA 'ii' or 'iin'
'iu' takes the form of 'EVA iii' or 'iiin'
And so on.