to install an old orthography Malayalam Unicode font which is required to read the posts below]
ചില്ല് of a consonant is different from its conjunct forming form without inherant അ.
Phonetic difference
Consider the scenario: Vow + CC + Con.
Vow - a vowel
CC - a consonant capable of forming ചില്ല് - chillable :)
Con - a consonant
When CC takes its ചില്ല് form, it is joins more with Vow. This effect produces a noticable small stop between CC and Con.
When CC takes its conjunct forming form without inherant അ, it joins more with Con.
Examples:
ഉണര്വ് ഉണര്വ് (unlike its pair, not a meaningful word)
കല്വിളക്ക് വില്വാദ്രി
കണ്വട്ടം കണ്വന്
Reference: കേരളപാണിനീയം, പീഠിക - A. R. Raja Raja Varma