We're creating an alternate history mod where the Qing are still around. While I wouldn't say that we "ignore objective historical facts", we do make assumptions in order to rationalize certain outcomes. As I said earlier, in order to keep KR china recognizable, we decided that the preservation of certain elements was key. This involves some backwards-rationalization.
The Guominjun are meant to be significantly weaker in this timeline even before the Northern Expedition, their main army under Feng Yuxiang historically held off the Fengtian Army around Zhangjiakou thanks to Soviet aid, and in particular their construction of concrete fortifications. Without that aid the Guominjun never make serious inroads beyond Sanmenxia into Henan, and they're barely holding on in South Chahar. As Fengtian's armies rush south to deal with Wu Peifu's unexpected advance toward Beijing, Mongolian forces sweep in from the opposite site. We also make a blanket assumption that progressive movements like Feng's, no matter how genuinely progressive he actually was, are somewhat weaker KRTL due to the success of German militarism in Europe and the collapse of the Western democracies.
The French are meant to have played quite an active role in supporting the KMT, one comparable to the Soviet Union OTL. It's not just advisors and Russian exiles, but also funds and weapons. Also, the KMT do mostly lose the war on their own, the Germans don't provide a ton of support.
It's harder for me to comment here because my area of expertise is really North China, but my understanding is that the rationale for Yang Sen's presence isn't so much that the conference was a success, but rather that he was selected and then backed by Beijing due to his Zhili ties. He's barely hanging on to de-jure leadership of the province, and gets thrown out in the vast majority of games.
As for Lu Rongting and Chen Jiongming, the idea is that Sun Chuanfang (and by extension Wu Peifu and the Germans) prefers to keep them at loggerheads, instead of creating a unified southern clique that could threaten his rule in Nanjing. They're set against each other, and also against Sun.
Well, it doesn't necessarily lead to a ceasefire on all fronts, just the movement of the main armies. With the timeline and the Northern Expedition writeup we're always covering the major actors, and assuming there's smaller scale action happening at a level that's less important for us to cover. Also, Sun's provinces do reject rule by Wu Peifu's government in the north. The state of "unification" is mostly de-jure, which is why we say that the Qing Government's control is mostly limited to the North China Plain.
It is a hollow gesture. He doesn't see them as a serious problem, and considering the shockingly bad administrator he was, that doesn't seem unreasonable to me.
It doesn't remain at peace for 7 years, there's the Shanghai Uprising, and presumably smaller conflicts between warlords. As for the major actors, you're right that the cliques aren't dependent on the Qing government, which is why(as I mentioned above) the "unification" is mainly de-jure. The primary factors preventing conflict between the major factions are:
1. The risk of starting a regional war. The situation in China resembles a sort of frozen conflict, where Germany and Japan are squaring off against each other, but benefit too much from the status-quo to start anything. Japan gets to keep a fairly secure Manchuria, agreed to by international treaty, Germany gets to subvert the Legation Treaty via the AOG, and the United States gets to formally uphold the "Open Door Policy" while taking its own share of the pie. The risk of the United States siding against an aggressor is also a major factor for either Germany or Japan. As a result there's a fair amount of pressure on the parties within China to uphold this status quo if they want to keep the aid they're receiving, and Sun Chuanfang (who is the nearest sub-national competitor to Wu in terms of strength) is particularly dependent on German aid. The natural thing for him to do would be to side with Zhang Zuolin against Wu Peifu, but German pressure makes that impossible.
2. The concentration of heavy weapons in only a few hands. Unlike OTL where China was subject to arms treaties making the import of heavy weapons difficult, those treaties don't exist in this timeline, meaning that the foreign-aligned factions in Beijing, Nanjing, and Shenyang are significantly better equipped than in the inland and non-aligned factions like Shanxi. This means that those smaller poorly equipped cliques will have a hard time banding together against the status-quo factions.
3. The Legation Cities. The main purpose of the "Neutral Zones" surrounding the Legation Cities, beyond providing them with protection, is denying the major warlord cliques the opportunity to exercise control over key logistical and financial centers like Tianjin and Shanghai. This reduces avenues for competition, and means that a major north-south war will need to take place almost solely on, or in the vicinity of, the Jinghan Railway - almost guaranteeing a stalemate.
Even with all this, though, China is meant to be like tempered glass at game-start. All it takes is some unrest and an assassination to send everything spiraling out of control. From there forward everything is game-design more than it's alternate history.
