There is a lot to respond to.
But perhaps the most important consideration is accessibility - your reduced vision.
If you run the command
you see the list of Atom packages installed (Core and Community sets).
You can experiment with dark themes which might be better than light themes.
Investigate tweaking styles.less to change environment such as font size, colours. Edit > Stylesheet.
Now we turn to Mathematica.
I have a number of development experiments underway, using Atom at the core. Mathematica is on my “to do list” and I had already installed wolframscript. Currently I am studying workflows integrating Julia + R + Jupyter Notebooks.
But I can break off this for a while and look at Mathematica. I will be using Mathematica later in my project plans, so it helps my own thinking.
I have explained that I am on Ubuntu 20.04 and so my workflow will differ from Windows. But the same principles apply.
Principle explained so far:
Atom can be part of an engine of microservices.
My view is - dispense with the idea that Atom should be a “one stop shop hackable editor”. Instead, Atom can be part of an ecosystem where other tools and microservices interact - through process-palette as the connector.
Atom can be the primary editor of resources, but editorial control over any file might be passed to another cooperating microservice (desktop or cloud).
I already apply this thinking in interacting with IntelliJ IDEA. But for Java rather than Mathematica. I have now installed the extensions for Mathematica and Wolfram Language. However they require subscription accounts.
We can consider how to connect Atom to IntelliJ IDEA. I have no plans so far to use Eclipse. I have also tried NetBeans.
Using common resources
Thus we start with shared folders and files and assets. This can be in Github or in project folders. They might be in Dropbox folder if shared with cloud based services such as webMathematica.
We might start editing a file in Atom but then pass control to an IDE such as IntelliJ IDEA. These two worlds - Atom and IntelliJ IDEA - do provide a considerable degree of overlap of functionality. But the principle of collaborative working - considering these IDE’s as microservices - can work well. We can even pass control from Atom to VSCode.
The small utility I suggested - Actiona - acts as an important helper in the automation.
Tip: Using Actiona script, Atom and other IDE’s might be arranged to appear in different desktop virtual workspaces. This makes it easier to toggle between these desktop virtual workspaces.
I suggest that you first install Actiona as I proposed. Then when you have done this, confirm back here, and I can follow up later with workflows as scripts.
Regarding suggestions on the list of Atom packages to support Wolfram Language, you might leverage packages for autocompletion (emmet) and adding snippets of Wolfram code.
Search “wolfram” in packages to review packages to try.
One advantage of passing automation scripts between cooperating users (remote team members) is that you apply these to your real instance of Atom/Mathematica/IntelliJ. This is an improvement over squinting at screencasts in YouTube. Of course the source of such scripts (executable bots) should be trusted since they have potential to cause damage if applied without thinking. Less risk if you develop your own automation scripts using the GUI.