The biggest problem with a lot of northern languages is the awful schwa deletion. Even the Marathi of Maharashtra is subject to it. Strangely, the Marathi of Thanjavur has far, far less of it from what little I have heard of it.
Sanskrit does not do schwa deletion. So engines must map the phonemes to Kannada/Telugu (which support the full complement of Sanskrit sounds) if they want to get somewhere. A lot of this can be solved if the backend supports ipa.
But this is for classical Sanskrit. Vedic recitation is too complex (and I know too little about it) to handle without a LOT of work.