I think you are thinking in more drastic terms than me. I am not talking about ethnic mongols in Inner Mongolia somehow declaring independence. That will never happen. But what can happen is what was happening in Xinjiang, which is separatism, animosity between Han and Mongols, terrorism, destabilization. Its just adds more challenges for China's development. It doesn't matter how dirt poor Mongolians are, they can still foment ideas of ethnic glory, terrorism and separatism.
Xinjiang is very different from Inner Mongolia. First of all, if you look at the population distribution, Xinjiang is a remote outpost compare to Inner Mongolia. The Han Chinese population has never been the majority in Xinjiang, making it a real non-Han ethnic majority. Xinjiang also has a very different culture, religion and race from the rest of the country.
Mongolian are mongoloid, same as Han Chinese, Tibetans, Manchu, south western Chinese minorities (Hmong, Zhuang, etc), while Uyghur, Tajiki (Pamiris) etc are caucasoid. In terms of religion and culture, both Mongols and Han Chinese, along with Hmong, Zhuang, Tibetans are Buddhists, with a past of shamanism/animism.
Inner Mongolia has been the front line of Sino-soviet confrontation for decades. A lot of China's heavy ground force weapon/equipment production facilities are in Inner Mongolia. When it comes to transportation, Inner Mongolia is by no mean an outpost, it is as inter connected with North China Plain as other major population centers in China.
Extremism and terrorism in Xinjiang are propagated under the guise of religion. While in Inner Mongolia, there are no such religion issue. Buddhism is not the same as Islam. In Buddhism, only Monks find it in themselves to act out political activism. A buddhist is not necessarily a Monk. Most believers of Buddhism are NOT monks, they are patrons/donors of Buddhism (施主). While in Islam, every believer is a Muslim. Muslim are obliged under their religious duty to fight for their religion, while patron/donors of Buddhism (施主) are not, even though both are technically the believers of their respective religions. Therefore, it is much easier to incite Muslims to participate in a Holy War, than Buddhists. In fact, I know not any such "Buddhist Holy Wars" even exists.