to install an old orthography Malayalam Unicode font which is required to read the posts below]
When C1 + VA is represented with subscript form of VA, then it means, C1 is actually Chillu-C1; but couldn't be written that way because Chillu-C1 is deprecated.
Correspondingly, for these clusters, VA is not pronounced as semi-vowel-va; instead it is pronounced in 'full'. In Malayalam, യ and ഴ are capable of forming chillu along with others - ന, ണ, റ, ര, ക etc. Among them, Chillu-ഴ exists only in 'very old' words. Chillu-യ is seen no-where. So, C1 can either be ഴ or യ. That infact is the case. The 'zhva' and 'yva' are the only two clusters represented with stacked വ subscript.