Gunslinger, you bring up some valid points. Motor mount locations on the chassis and block are interesting to think about with regard to clearances. An R3 parallel would be the Granatellis lowered RS1021 in 1025, whereas on the production R3's they shimmed up the body.
Another area where I have experience was when I had a '69 Vette, looking through catalogs like Summit for intake manifolds. I had to be alert for the footnote, Will not clear stock Corvette hood. I probably could have gone with a repro L88 hood, though hood replacement is but one solution and must be factored in to the budget.
One of my friends made fun of the "salad bowl" the Ford Thunderbolt cars had, especially when another friend was modifying the engine in his Chevelle. The jokester would dole out a good ribbing, "You're going to have to put a salad bowl in your hood, your modifications won't fit otherwise 😆" The Chevelle's mod. list altered and no salad bowl was needed. Ford however, needed that bulge and it's there for good reason.