No, the HMM is not replaced in that work. The GMM is replaced, as you surmise. There are three problems with standard ASR: HMMs, GMMs, and n-gram language model

No, the HMM is not replaced in that work. The GMM is replaced, as you surmise. There are three problems with standard ASR: HMMs, GMMs, and n-gram language models. The GMM is the easiest to remove. Keeping the HMM allows simple, efficient decoding algorithms.