Is the establishment of proof limited to the ruler, to the exclusion of the knowledgeable mujtahid scholar? And how does this reconcile with scholars like Ibn Taymiyyah declaring specific innovators, such as Ibn Arabi and Al-Hallaj, to be disbelievers?

The one who establishes the proof (hujjah) is he who possesses knowledge of it and is capable of establishing it. These are the people of knowledge and understanding of the Book (Quran) and the Sunnah, and what the righteous predecessors were upon. This matter must be referred to the well-grounded scholars and the legitimate (Sharia) judges, because declaring a specific individual to be a disbeliever (takfir al-mu'ayyan) is a serious matter that must be governed by its Sharia controls and entrusted to those qualified for it. They are the ones legally competent to examine the conditions and impediments and to understand the circumstances of people.