The Gun Devil was only ever feared at this level because other horrors, which Pochita had erased,
such as nuclear weapons, an in-universe volcanic eruption, and a starlight that would break children's minds, along with pieces of the War Devil, were gone. This was so extreme that
there hasn't been a single war since World War II, and war became a concept limited to movies and video games. The fact that the Nuclear Weapons Devil, along with a devil representing volcanic eruptions and even a certain starlight, had been erased, and people no longer feared different conclusions other than death, played a huge role in this shift.
In reality, with most of these terrible concepts gone, including WWII and Nazis, the world was already at a state of relative peace, with fewer things left to fear compared to what was once feared in the real world. Guns remained unaffected by this, so when something catastrophic like the Gun Devil's appearance occurred, it triggered a massive response. Had the devils Pochita erased still existed, the repercussions of the Gun Devil's appearance wouldn't have been as grand. This means that the argument of Pochita being the devil all devils fear the most is valid enough to hold a higher place than even the 100% Gun Devil.
All of the battles Makima fought were ones she carefully prepared for, which is why the gradual weakening of Pochita over time was successful. With an extended amount of preparation, she even rendered Pochita unbeatable and had to resort to completely stripping his power away to even stand a chance. You could even argue that Makima's timing and preparation to weaken Pochita was more meticulous than in her fight with the Gun Devil. In fact,
this was something the Future Devil had foreseen. Every action, apart from her eventual defeat, was orchestrated by her. Pochita's summoning, his depowering, and his eventual downfall. Need I say more?
The spear impaling Pochita isn't as much of an anti-feat as you make it seem, considering he's the only hybrid who can even harm Pochita, which means the weapons scale higher than his physical stats. Using the finger gun against the 20% Gun Devil is also a poor comparison, given the circumstances of the fight. It took place at a great distance,
and we know the Gun Devil can regenerate over time. Plus, her goal wasn’t to kill him, but to get him as close to death as possible and force him into Aki’s body if he wanted to survive, so she could continue with her plan.
As for why she chose the Weapon Devils to fight instead of using her overpowered devil kit, it’s because of the elaborate depowerment plan she had in place for that specific moment. Notice how she even holds Pochita in higher regard than the Gun Devil?
Current Pochita will get his own key at the end of Part 2. And Spear scaling above the gun doesn't necessarily have any qualms in my eyes.