A few related points. First, the issue with Murty Sanskrit and the l with dot below and macron is of course a font issue. Simply: the font is missing the glyph at U+1E39, which is exactly LATIN SMALL LETTER L WITH DOT BELOW AND MACRON I'll try to give the developers of that font a heads-up.
Just to double-check what Windows does with these fonts, I installed all of them on a Windows 10 system, and opened the attached HTML file. Except for that one letter in Murty, they look fine. About GNU FreeFont: again, there were some inconsistencies, but I overreacted. I'm going to pull back some of the changes I made, intending to fix a problem that wasn't there. Cheers!Title: sanskrit marks
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ