Thanks for the example; it's not a language I've worked in recently. I find it odd that the Mukta Vaani font you're using only works when it's not marked with the appropriate language. I tried a variety of other Gujarati fonts, and none of them behaved in this way. The fonts that rendered differently under different text shaping engines dropped the combining mark when the Legacy Text Shaping engine was turned on. So Mukta Vaani is the outlier, here. How important is it to you to use this font in particular? Can you reproduce the same issue with a different font? Can you reproduce this issue in another application that uses the same Harfbuzz text shaping engine? (I can't, for what it's worth; so long as I don't mark the text as Gujarati, this font seems to work fine in Scribus.)
To jump to the end of this conversation, if it can be demonstrated that this is a problem with the way that InDesign in particular is handling this font, and that it's not a problem with the font, then the way to ask for a bugfix is to go to indesign.uservoice.com and submit a bug report there. Gathering votes for your post there is the fastest way to get this issue in front of the eyes of the developers.