This can be a confusing topic to someone new to circuits, especially those we see in our valve amps. And while Merlin is an established expert, and I generally agree with his advice, I think the chapter you are referencing is difficult to understand for many readers (including me).
Am I wrong in concluding that, in the diagram provided, the can seems to be connected to chassis ground with the Mains earth ground?
No, you are not wrong. The key to understanding this is in the first page or two of Merlin's grounding chapter, when he admonishes us to think about current, which does NOT normally flow from the chassis ground to the Mains Earth Ground.
Furthermore, is the separation of grounds in the schematic to minimize noise?
Yes.
Would tying the two grounds together effectively remove the earth by tying the Mains neutral and earth together?
Well, no. Recall that Mains neutral (this is the white wire in the USA) is tied to one of the primary windings of the PT, and is NOT tied to ground.
It is true that chassis plays a role in most guitar valve amps circuits by functioning as a "return" for the secondary windings, but it is NOT functioning in this manner for the primary windings (to which it should not be tied).
There is NO single grounding system that works every time. However, if you pay attention to Doug's grounding scheme as outlined in his build documents, it is very reliable. In general, ground your power amp section close to the transformer, and ground your pre-amp as far away from that as you can, generally close to your grounded input jacks in a Fender style amp.
Best of luck, and have faith you will enjoy the journey!