To be clear, the OpenFlexure project is quite awesome and I am planning to build my own "garage" microscope sometime, and this design is the lead candidate. Two things you _cannot_ skimp on in a decent microscope, however, are a good objective and a good camera, and they both cost in the thousands at the least.
The constant struggle with biological microscopy (and I suppose most imaging technologies) is to try and extract the most amount of information possible for every photon your sample gives out. This will simultaneously allow you to observe samples without affecting them too much and get higher spatiotemporal resolution.
The whole field of superresolution started because we thought we hit the fundamental theoretical limits of how much resolution we can get from _any_ light microscope, even when using the cutting edge imaging technology. Superresolution techniques tried to trick and work around the limit by adding some extra imaging criteria (image one molecule at a time, screw with the illumination psf, fancy fluorescent proteins, etc). If you use suboptimal optics and then apply superresolution techniques, the image quality you get would just be worse with superresolution in this setup than with a regular microscope with good optics. That is actually clear in the figures in this paper - the "superresolution" images in the paper are worse than what any regular graduate student would get from a department confocal microscope.
Can't fault the particular study though: the entire superresolution microscopy field was a multibillion dollar blackhole of research funds with almost nothing to show by way of meaningful biological insight (leave alone deserving of Nobel prizes so soon).