Thanks much for the detailed info!
Regarding the general style, I would be interested in what you consider to be a good, more modern one, using the examples at
http://www.wazu.jp/gallery/Fonts_Devanagari.html
Apple has been using the old style for a very long time now, but it may be worth asking for a change. They recently did that with Thai (although this has also generated complaints from those used to the old style).
Regarding the conjuncts, it appears that Devanagari Sangam always uses the wrong glyph for the "eyelash RA". Definitely a bug that should be reported to Apple. Here are some older bugs which I have not had time to recheck with 10.9 yet:
http://m10lmac.blogspot.com/2013/08/bug-in-apple-devanagari-fonts.html
To report these problems to Apple, use
http://www.apple.com/feedback