I'd be willing to bet that even if Microsoft did create VSCode for the purposes of cutting Github's expansion, the effect that VSCode had on Github's valuation is extremely overstated here. The total valuation comes from a range of factors, but let's say there are two major ones: number of users and number of paying organizations. The latter is almost completely not dependent on Atom (companies would not use Atom as a deciding factor to use Github) and while some users might use Github because they used Atom first, I don't think that this is large enough that the migration from Atom to VSCode negatively impacted the valuation.
I think a simpler explanation is correct: Microsoft saw that open source developer tools are gaining a lot of popularity and also knew that it could help revitalize/modernize their image, so they authorized the funding for the creation of a (mostly) open source code editor, and it gained popularity because it was good.
The revenue generating upsell for VSCode is already here and it IS GitHub Codespaces. They are going to add features you can't live without based off code synthesis (sky's really the limit here) and gate those off saying it can't run locally because it's too resource intensive. They'll charge you (or your company) by the second for all usage.
It would be much harder or impossible for them to do this if Atom and an independent GitHub had been further entrenching in this space for the last decade.
Many of the biggest developer tooling projects big corp are building now existentially threaten smaller developers and apps, by design.
Don't give Microsoft a pass here.