Ligatures are always a little confusing. But in all honesty, I think it's not unreasonable that the native speakers adapt just as computers adapt, and we meet somewhere in the middle. In some ways it seems gross that we change an entire language and tradition to comply with our technical limitations. But people have been doing that for thousands of years, and they'll do it today regardless of whether it is expected or approved. Spanish officially dropped two letters a few years ago (ch and ll) in recognition of the predominant understanding of what a "letter" is. If I remember correctly, Chinese is traditionally written top-to-bottom, but electronically it seems like left-to-right is the norm. I appreciate the adaptation. Not because everything should match the Western norms, but because the Western norms are notable for how much they themselves have adapted over time, and I believe there's virtue in that.
If Devanagari adapts its ideas of the linguistic meaning of character, or readers recognize the adapted typography of that character, I think that's reasonable. But then I'm not a traditionalist, and I like the idea of a polyglot.
I agree it's an inherently difficult problem. If you're not going to give ligatures their own code points - I assume native speakers were probably consulted and said "no" to that idea - then you have to come up with something. And the something thery came up with is perfectly reasonable.
It still leave us, though, in the situation where there are plausible arguments for the "length" of a single sequence of three code points being one, two -or- three, with my personal preference being two.