It is really annoying that you're shifting the goal post by bringing up Wikipedia (as an example, not the article), which is very much different from Github in many ways. Still, Wikipedia is not a common good in my book, but at least in the case of Wikipedia I can understand the reasoning and it's a much more interesting case.
But let's stick with Github. On which of the following statements can we agree?
Z1) A "Commons" is a system of interacting market participants, governed by shared interests and incentives (and sometimes shared ownership). Github, a multi billion subsidiary of the multi trillion dollar company Microsoft, and I, their customer, are not members of the same commons; we don't share many interests, we have vastly different incentives, and we certainly do not share any ownership. We have a legally binding contract that each side can cancel within the boundaries of said contract under the applicable law.
Z2) A tragedy in the sense of the Tragedy of the Commons is that something bad happens even though everyone can have the best intentions, because the system lacks a mechanism would allow to a) coordinate interests and incentives across time, and b) to reward sustainable behavior instead of punishing it.
A) Github giving away stuff for free while covering the cost does not constitute a common good from...
1. a legal perspective
2. an ethical perspective
3. an economic perspective
B) If a free tier is successful, a profit maximizing company with a market penetration far from saturation will increase the resources provided in total, while there is no such mechanism or incentive for any participant in a market involving a common good, e.g. there will be no one providing additional pasture for free if an Allmende is already destroying the existing pasture through overgrazing.
C) If a free tier is unsuccessful because it costs more than it enables in new revenue, a company can simply shut it down – no tragedy involved. No server has been depreciated, no software destroyed, no user lost their share of a commonly owned good.
D) More users of a free tier reduce net loss / increase net earnings per free user for the provider, while more cattle grazing on a pasture decrease net earnings / increase net loss per cow.
E) If I use less of Github, you don't have any incentive to use more of it. This is the opposite of a commons, where one participant taking less of it puts out an incentive to everybody else to take their place and take more of it.
F) A service that you pay for with your data, your attention, your personal or company brand and reach (e.g. with public repositories), is not really free.
G) The tiny product samples that you can get for free in perfume shops do not constitute a common good, even though they are limited, "free" for the user, and presumably beneficial even for people not involved in the transaction. If you think they were a common good, what about Nestlé offering Cheerios with +25% more for free? Are those 20% a common good just because they are free? Where do you draw the line? Paying with data, attention, and brand + reach is fine, but paying for only 80% of the produce is not fine?
H) The concepts of "moral hazard" and "free riders" apply to all your examples, both Github and Wikipedia. The concept of a Commons (capital C) is neither necessary nor helpful in describing the problems that you want to describe wrt to free services provided by either Github of Wikipedia.