They are using Baraha for composing.
Somewhere,
a note says:
--------------
The letters are converted as per standards provided in Baraha Software
which is BRH Devanagari Extra for Sanskrit, BRH Malayalam Tab Extra
for Malayalam.
In Tamil the font was not found very attractive and therefore we go through
additional conversion process from standard Font to Latha Font provided
by Google.
3 Special notes for Tamil book readers
To represent the four variants of க, ச, ட,த, ப
The number is given as the lowered scripts after the letter e.g க2, த3, ப4
to represent that it
is second, third or fourth variant (varNa).
----
I sent mail to them to share their above conversion, no news, trade secret?
As you now know, Baraha version 10.10.800 (64 bit) supports subscripts.
Also note:
When a Sanskrit word ends with anusvara (M) and has a vedic tone (svarita, deerga svarita, anudatta), what is the correct way to write it in Tamil?
- vedic tone on ம்ʼ
- vedic tone on previous letter
अव॑तु व॒क्तारं᳚ அவ॑து வ॒க்தாரம்᳚ʼ OR அவ॑து வ॒க்தார᳚ம்ʼ
यच्च भव्यं᳚ யச்ச ப₄வ்யம்᳚ʼ OR யச்ச ப₄வ்ய᳚ம்ʼ
In aksharamukha conversion of the above Sanskrit words, the vedic svara appears on ம்ʼ only like ம்᳚ʼ, as shown above.
But vedavms.in and prapatti.com, it appears on previous letter:

Reason for my doubt: Please ref page 10-11 of the attached doc.