(quotes taken from Houlgate's Book, 'An Introduction to Hegel')
Hegel thinks that thought and reality are going to grow together in ever increasing clarity. Houlgate notes that some might think this to be presumptuous: "How can thought be certain that it is able to bridge the gap between itself and being and disclose the true nature of what there is?" (p. 45) But, he continues, for Hegel this is a bad question, because it assumes that there is a gap between thought and being in the first place, and not, instead, that the gap is between thought and itself — in other words, the problem is not that thought and being are separate, but rather that thought has not, in its incomplete stages, understood the unity between itself and being.
But does this not amount to the same thing said in a different way? Not necessarily. In the first instance, what is and what we think about that reality are disconnected from each other by a structural deficiency that is ultimately unbridgeable by either reality or thought. In the second (Hegelian) instance, reality and thought are primordially and ontologically connected — indeed, united — but there is a disconnect within thought itself which does not allow thought to recognize this unity, since it has been too quick to assume that the categories by which thought functions (i.e., our logical principles) must be the absolutely correct way of understanding the world, which leads to the resulting blindness that is incorrectly perceived as a disconnect between thought and that world.
But, likewise, this means that if Hegel is going to be consistent, he will not — and indeed Houlgate thinks he does not — make any absolute claim about the fundamental unity of thought and reality at the start of his logic either. For to do so would be to start with an unnecessary presupposition that cannot be justified. Thus, because "we can presuppose no conceivable distinction between thought and being at the beginning of the Logic, the categories set out in the Logic must be ontological. At the same time they cannot provide a description of any Absolute, reality or being that is presupposed as the distinct, given object of philosophical enquiry." (p. 45)
What, then, do we make of Hegel's statements that the end of the system is the beginning, and vice versa? Are we simply to take Hegel at his word that the discovery of 'Absolute Being' is something that he did not conceive of prior to reaching the end of his system, and that it is merely coincidental that the fact of Absolute Being as the end of the system means that such unity and conceptual truth is also the beginning of the system? It seems too convenient... at least that's my impression.