This is actually a rather fascinating subject and an excellent question, as it is not commonly assessed or written about from a western perspective. However I will attempt, with due diligence to preserve impartiality as to remove any perspective skew. The threat lies in a plethora of overlapping and coinciding issues, which each serve to contribute towards one another in a compounding domino effect of consequences, either potential or formulating in actual conflict and a threat towards Russian national integrity.
The baseline factor of the importance, and from this, the threat of loss through separatism within the region lies within the bountiful mineral wealth of the Siberian regions.^(1) The land mass is abundant in highly sought after oil, gas, ore and timber^(2), as well as serving as a surprising fertile agriculture zone in the Far Eastern Siberian regions.^(3) This particular baseline contributes towards post-Soviet sentiment of the gravity of the loss through separatist movements. An assessment of the post-Soviet mindset will not be complete without the preceding mindset of the USSR of course.
The following factors encompass a period that threads the line between 20th century and modern to contemporary history, so may be in breach of the subreddit rules, but alas I shall ensure that it is capped to a minimum mention at the end of my answer. The threat level was indeed present and very tentative, with tensions flaring and sparking in the mid 20th century, with the 1969 border conflict with China, after the Sino-Soviet split.^(4) This situation was resolved in 1991^(5), ratified in 2005^(6), and again in 2008^(7), with the two sides agreeing on border lines. However this agreement only amounted to a compounding of Chinese economic mobilization and thus political disaffection occurring on both sides in different forms. It is in both countries interest to stir up separatist sentiment in border regions as to ensure an ease of beneficial economic expansion and access into those resources and areas by applying countermeasure pressure which lead to eventual economic concessions and a furtherance of delimitation, with Xinjiang Uyghurs in China^(8.) and disenfranchised citizens of Siberian regions.^(9) More so for China, as their economic output is rapidly expanding, and so is their need for resources. There have been multiple agreements signed which allow the Chinese to work within Russian Siberian regions, in the areas of agriculture, forestry and animal husbandry, expanding into mining. ^(10) This suits Russia well due to the logistical problems of extracting primary resources from their remote Siberian territories, with China investing a sustained subsidy of 100 billion yuan towards infrastructure in the region and a further 10 billion USD investment being announced at this years belt and road conference.^(11)
The threat comes primarily from dissent towards Moscow from the population of the Siberian citizens, which contain 16 million people, this dissent is derived from economic factors of the Soviet and post Soviet era, with resources being extracted yet infrastructure and subsidies for local amenities of the population severely lacking, added towards the fact that living wage is low, along with quality of life, for such a wealthy mineral rich region, this creates political dissatisfaction.^(12) This sentiment is indeed a threat toward a post Soviet integral nation, as dissatisfaction leads towards a possible move to greater autonomy for these regions. This greater autonomy will allow the populace to reap further benefits from economic co-operation from China in the far eastern regions, as they can raise the paltry amount of land rental rates that government sanctioned management companies have leased at exorbitantly low rates.^(13) Post Soviet Russia now balances the plates of political reactionary elections within their Siberian regions, with a communist governor being elected in Khakassia and a far right LDPR official being elected within the region of Khabarovsk.^(14) Each of these elements play a role in adding towards the possible threat of separatism, economically or politically. As on one hand the dissatisfaction towards the current United Russia party of Moscow may lead toward a regional led insular pivot of operations in Khakassia and Khabarovsk, which would not be conducive towards the ideology of leading Moscow government^(15) and would threaten the economic unity of the Siberian regions doing business with China, which they see as a threat towards the economic benefits of their populace due to the Chinese tendency of rapid and intense resource extraction.^(16)
So to sum up without stepping over the sub rules for proximity to current affairs, the region is indeed highly valuable towards the economic trajectory of the Russian state, and thus any infringement towards the post Soviet ideal of Russian unity is perceived as a threat, economic, political or otherwise. Is it as much as a threat as say Chechnya ? , most definitely not, as the threat lies in an economic baseline,as opposed to one mired in centuries of ethno-religious strife.
Shabad, Theodore and Mote, Victor L. Gateway to Siberian Resources , p.27
Velikanov, Nikolai, Soviet Military Review 1986, p.8
Kotkin, Stephen, Wolff, David, Rediscovering Russia in Asia: Siberia and the Russian Far East: Siberia and the Russian Far East, p.35
Yang, Kuisong, "The Sino-Soviet Border Clash of 1969: From Zhenbao Island to Sino-American Rapprochement" in Cold War History , p.21-52
Akihiro, Iwashita, "An Inquiry for New Thinking on the Border Dispute: Backgrounds of "Historic Success" for the Sino-Russian Negotiations" in Slavic Eurasian Studies 6. p. 95–114
"China, Russia solve all border disputes". Xinhua. 2 June 2005
"China, Russia complete border survey, determination". Xinhua. 21 July 2008
Gladney, Dru C. , ''Islam in China: Accommodation or Separatism?'', in The China Quarterly No. 174, p.457
Lomanov, Alexander, China Inside Out: Contemporary Chinese Nationalism and Transnationalism, p.86
Stroski, Paul, ''Cooperation and Competition: Russia and China in Central Asia, the Russian Far East, and the Arctic'', in Carnegie Endowment for International Peace Feb 2018, p. 2
''Chinese in the Russian Far East: A Geopolitical Time Bomb?''. South China Morning Post, 7 July 2017
''Irkutsk in the spotlight: the leak in Putin's watertight system?'' The Guardian, 16 March 2018
Red governor: Communist to lead Russia’s region in Siberia after being only runner on ballots, Russia Today, 11 November 2018
Hale, Henry E., "The Origins of United Russia and the Putin Presidency: The Role of Contingency in Party-System Development", in Demokratizatsiya. 12, p. 169–194.
Cons, Jason, Eilenberg, Michael, Frontier Assemblages: The Emergent Politics of Resource Frontiers in Asia, p.163
About a year ago, I asked this same question, and I received some responses.