One of Lowell's contemporaries conducted an experiment where cardboard circles covered with random splotches and markings and illuminated to simulate the telescopic appearance of Mars were shown to students who were asked to draw them. Many of the students sketched linear features similar to Mars' canals even though they weren't there. We know now that the human brain/eye "image enhancement" capabilities tend to create lines where none exist by joining disconnected dots at the limit of vision, or by edge-enhancing boundary zones between subtle shading differences. Lowell's reputation for visual acuity and the quality of his telescope (and his apparently exaggerated opinion of the seeing in Flagstaff) apparently trumped these critics.

As for the issues brought up in the S&T article, I don't know. I have severe presbyopia and wear reading glasses but I have extremely acute distance vision. At my age, I am very familiar with "floaters" and other geezer-related eyeball artifacts that tend to show up at extremely high magnifications, and I find it difficult to see how Lowell wasn't on guard against them. As for his technique of stopping down his objective, I have reservations about that, too. Stopping down can be of value when atmospheric ripples are of a size where they resonate with the diffraction rings of a lens, so sometimes stopping down can help sharpen up an image, but the price you pay is that you lose some of the lens' resolving power. The Flagstaff Clark objective was of extremely high quality, as good as any built today, its performance shouldn't have been improved by restricting its exposure to the truest central portion of it.

All else being equal, seeing effects, even on the best nights and sites, limit the maximum magnification for planetary work to about 400X regardless of the telescope used, so the diffraction-limited theoretical maximum magnification of the Clark objective of about 60X per inch of aperture would never have been achievable anyway, at least for planetary observing. (For faint stars or nebulae you throw as much aperture as you can get at the problem because light-gathering, not resolution, is what you're trying to optimize.)

BTW, as a quick rule of thumb for amateur 'scopes, the lower and upper magnification limits
for a telescope objective are between 0.2 and 2.0 multiplied by the aperture in millimeters. For my 4 inch (100mm) 'scope, magnifications below 20x will chop off part of the light cone and will not result in brighter images, and magnifications exceeding 200X will show no additional detail. These are physical limitations due to the optics of lenses and the wave nature of light. A cheap, poorly made lens will not reach these limits, nor will the most expensive high quality objective exceed it. When you buy eyepieces, you should restrict the selection to oculars yielding magnifications in this range.