Essentially, what I have shown in the challenge is that the issue of (chillu ? chandrakkala) is not a derivative of the issue of (chandrakkala ? samvruthokaaram). These issues have to be tackled separately. So I am taking (chillu ? chandrakkala) alone now.
In the challenge, the words differ precisely in /nn/ and /n_n/ location. We know, in the phoneme space they are different. That is, dental ന + dental ന and alveolar ന + dental ന. How is this distinction is indicated in orthography? Before explaining that, let us look at chandrakkala once more.
Chandrakkala when used for vowellessness, is acting as a language specific control character. It removes the default 'അ' from the consonant behind it. That is, it is acting as an attribute remover.
It is the property of any vowelless consonant to get help from the consonant next to it as if that is a vowel and thus creating a conjunct. In /n_n/, this specific property is prevented. That is how alveolar n and dental n can stay close without conjunct forming transformations. How are we denoting the removal of this conjunct creation property? Are we using any specific symbols to indicate this? In fact, yes. It is a vertical tail across the letter.
Since chandrakkala exist as a separate orthographic entity detached from the letter, we can easy see its functionality. In contrast, conjunct creation preventer symbol get embedded in the orthography of a letter and that makes it difficult to recognize it.
So my conclusion (not a solution) is this: an malayalam specific control symbol, different from chandrakkala, is present in a chillu letter. Its functionality is 1) remove the inherent അ vowel 2) then prevent the consonant from forming deep conjunct with the next letter. If we recognize, the function (1) alone, we will not solve the riddle of chillu.
This symbol could be encoded as level-1 ignorable in the collation table, as most of the diacritic marks.