According to the example in the article, the damage from cut and cover also displaces the sidewalks (so that customers of a business have to reach the business via alleys) and causes evacuations and flooding.
In the Roncesvalles neighbourhood of Toronto (not as dense as downtown, but still an extremely walkable and bikeable commercial district), they had a major section of street closed for surface rail replacement for a significant amount of time, and it was very hard on businesses in that stretch -- people just didn't go there because it was noisy and dirty and unpredictably hard to get to and from places.
I don't think the objection in built-up areas is (just?) about driving.
In the Roncesvalles neighbourhood of Toronto (not as dense as downtown, but still an extremely walkable and bikeable commercial district), they had a major section of street closed for surface rail replacement for a significant amount of time, and it was very hard on businesses in that stretch -- people just didn't go there because it was noisy and dirty and unpredictably hard to get to and from places.
I don't think the objection in built-up areas is (just?) about driving.