The “native vs learned” explanation would work if all borrowed words in Italian took the article
la, and all native words took
l' with elision. This generalisation is incorrect: the correct generalisation is that all words starting in a vowel take
l', and all other words take the full form. This feeds into the wider generalisation that in Italian, vowels are elided before other vowels, but not before consonants, though there's lexicalised apocope in words ending in /n, r, l/.
The “native vs learned” situation would be quite remarkable, and is really only possible in communities of deeply-entrenched diglossia: roughly, frequent language switching by speakers who speak both languages natively results in two different grammars inside the same language, with all borrowed words respecting the phonological system, syntax etc. of the speaker's other native language. Such cases have been described, IIRC. There are also cases of words obviously made up of foreign phonemes, which speakers try to pronounce more or less according to the original, e.g. Italian enjambement. In English, on the other hand, this is seen as very pretentious.
But in the normal case, speakers aren't aware where the words they use come from, whether they're borrowings or not. So when borrowings phonologically behave differently from native words, this is evidence that they're made up of different phonemes, but is not evidence that the speaker switches his entire grammar mid-sentence. Saying that the word is a borrowing is not therefore a grammatical explanation, but a historical fact that may or may not have any bearing on the grammar. Any such connection must be explained in terms of the grammar itself.
The correct grammatical, phonological generalisation of the usage of the masculine articles in Italian is that
un/il is used before words starting in a single consonant, while
uno/lo is used before consonant clusters and /ʎ ɲ ʃ t͡s d͡z/.
uno/lo also appears before /j/, but it's not a consonant cluster. Therefore it must be grouped together with /ʎ ɲ ʃ t͡s d͡z/, which are described as “self-geminate”. Some of them are actually pronounced as geminate in Tuscan, some aren't, but all of them behave phonologically as non-simple consonants. /j/ is just such a consonant – in most pronunciation it's not pronounced as geminate, but in some, like Romanesco, it's geminate both on the surface and underlyingly.
Whether it's pronounced as geminate is irrelevant to its underlying status, which is determined by its phonological behaviour such as the form of the article it selects. But the fact that it is pronounced as geminate in Romanesco supports the conclusion that it's geminate everywhere else as well, just not pronounced as such. Additional strong support for this conclusion is the fact that /j/ can never be pronounced as geminate in those varieties where it's not already always pronounced as geminate. This makes it clear that geminating it phonologically doesn't result in a change of surface pronunciation, so that surface pronunciation cannot be used as a counter-argument.
Now your observation on the difference between
la iena and
l'ieri is interesting and valuable, and it clearly suggests that the graphic <i> in these two words represents two different phonological entities – a vowel and a consonant. We've already seen that in the case of
Juventus. This isn't that surprising, because the Florentine <ie> comes from and corresponds to /ɛ/ in original Tuscan and in most varieties south of it, and so fits the classical definition of the diphthong, counting as a single vowel.
la jena, on the other hand, has been borrowed differently, as a vowel-consonant sequence, and that consonant is underlyingly geminate, but simple in the surface pronunciation.