to install an old orthography Malayalam Unicode font which is required to read the posts below]
Knowingly or unknowingly we have already encoded one chillu and that is Anuswara!
This fact is described in the formost grammar book of Malayalam: Keralapaanineeyam by A. R. Rajaraja Varma. See the relevant scan from the section peethika: 4.varnnavikaarangal
Translation of the underlined sentence: 'Anuswara is a chillu.'
Same opinion is echoed by L. J. Frohnmeyer:
(thanks to Eric Muller and Mahesh Pai)
The history of anuswara becoming chillu is something similar to that of how vowelless ത /ta/ became chillu ല /la/. Initialy anuswara came to Malayalam along with rest of the Sankrit package. Later Malayalam started to use it as chillu മ /ma/. Essentially, malayalam anuswara should not be confused with the functions of anuswara of Devanagiri. They both are different.
A R Rajaraja varma is not infallible. However, if you want to refute his arguments, you should put forward enough evidence from academic literature. Also, you should clarify what should be the relative position of Anuswara in collation.
Current scenario can be compared to, assigning codepoints for some vowel signs and then on a later thought, encoding rest of the vowel signs as VIRAMA + ZWJ + Vowel.
So, if chillu of മ /ma/ can be encoded, then why not rest of the chillus ?
I know this argument alone is not enough for encoding rest of the chillus. But given that our options are limited, this makes the arguments to encode chillus more compelling.