Hi Subbie,
The quibbles and subtle points you bring up I see very easily and clearly as being a part of the list of steps given at the start by Dr. Adequate. Specifically, you would want to include a modification of the hypothesis. This is clearly a part of the first step, "(1) Formulate a hypothesis." This your detail, is for me ridiculous. Keeping it simple (void of legalese) lends itself to wider application. The fine points are decided on an individual basis and any scientist will be able to correctly apply the scientific method for his specific situation or area of research. Peer review will show if the choices made, fit.
One common arrow in a cdesign proponentists's quiver is bringing forward some perceived flaw in the the ToE, or some perceived contradictory bit of evidence, as if it will bring the entire edifice tumbling to the ground. Almost invariably, the perceived problem is nonexistent, but I think it's very important to make clear that even if a genuine problem is discovered, no one single straw can break the back of the camel that is the ToE.
I could not disagree more with that final sentence. "Genuine problems" bring down hypotheses and theories. Assuming a hypothesis or theory generally fits,
tiny incongruences are the meat of trying to find out where a hypothesis or theory is flawed. The first part of your quote I see as true but those points too fit squarely, for me, in the outline Dr. Adequate gave.