Just take as given that the analysis is correct, and screening for rare Disease A on net has no effect on life expectancy. Almost no one actually gets Disease A, but everyone is screened for it, and that has some diffuse cost to life expectancy: Screen enough people enough times and someone will die in a car accident on the way to or from the doctor's office. More likely the screening crowds out other more net-beneficial medical testing or is taken as some false comfort to continue an unhealthy lifestyle.
Modern cancer treatment, especially for the most common types (i.e. the most likely to be screened for) is very good, even if the cancer is caught later due to lack of screening. So even the folks who catch it early due to screening don't incur a benefit in many cases, further pushing down the life-expectancy win on average.
Still: This is like saying home insurance is a bad deal because on average the insurance companies make money. Screening is an insurance policy (not a free one, to be sure) against a catastrophic outcome.
If you're a public health authority in a utilitarian and budget-constrained mindset, sure, don't encourage screenings by the logic and findings of this analysis. But I don't think individuals should consider on-average-LE-negative screenings as something to avoid.