Dear Madhav,
As far as I can see this is a problem with the font Sanskrit 2003 and it can't be solved without modifying the font but I think modifying a font is prohibited under copyright law.
But there are two other unicode devanagari fonts which are called "compatible with Sanskrit 2003" (by that I believe they mean that they have the same conjunct consonents as Sanskrit 2003). I have used one of them Chandas for many years and as far as I can see in Chandas there is no problem with viewing anusvara in those places it is obscured in Sanskrit2003 and you still get all the conjunct consonents that are available in Sanskrit2003.
Here is a link to the webpage with these fonts Chandas and Uttara.
Regards,
Harry Spier