The 3800 repos weren't exfiltrated from the compromised machine.
The malware (be it a VSCode plugin, an npm package, or whatever is next) simply slurps up all of the users private keys/tokens/env-vars it can find and sends this off somewhere covertly.
It's trivial to do this in a way to avoid detection. The small payload can be encrypted (so it can't be pattern matched) and then the destination can be one of millions of already compromised websites found via a google search and made to look like a small upload (it could even be chunked and uploaded via query parameters in a HTTP GET request).
The hackers receive the bundle of compromised tokens/keys and go look at what they give access to. Most of the time it's going to be someone's boring home network and a couple of public or private github repos. But every once in a while it's a developer who works at a big organisation (e.g. Github) with access to lots of private repos.
The hackers can then use the keys to clone all of the internal/private repos for that organisation that the compromised keys have access to. Some organisations may have alerts setup for this, but by the time they fire or are actioned upon the data will probably be downloaded. There's no re-auth or 2FA required for "git clone" in most organisations.
With this data the hackers have further options:
a) attempt to extort the company to pay a ransom on the promise of deleting the data
b) look for more access/keys/etc buried somewhere in the downloaded repos and see what else they can find with those
c) publish it for shits and giggles
d) try and make changes to further propagate the malware via similar or new attack vectors
e) analyse what has been downloaded to work out future attack vectors on the product itself
Right now Github (and others recently compromised in similar ways) will be thinking about what information is in those internal repos and what damage would it cause if that information became public, or what that information could be used to find out further down the line.
"Customer data should not be in a github repo" is all well and good, but if the customer data is actually stored in a database somewhere in AWS and there's even just one read-only access token stored somewhere in one private github repo, then there's a chance that the hackers will find that and exfiltrate the customer data that way.
Preventing the breach is hard. There will always be someone in an org who downloads and installs something on their dev machine that they shouldn't, or uses their dev machine for personal browsing, or playing games, or the company dev infra relies on something that is a known attack vector (like npm).
Preventing the exfiltration is virtually impossible. If you have a machine with access to the Internet and allow people to use a browser to google things then small payloads of data can be exfiltrated trivially. (I used to work somewhere where the dev network was air-gapped. The only way to get things onto it was typing it in, floppy or QIC-150 tape - in the days before USB memory sticks.)
Detecting the breach is nigh on impossible if the keys are not used egregiously. Sure some companies can limit access to things like Github to specific IPs, but it wouldn't take much for the malware to do something to work around this. (I can see things like a wireguard/tailscale client being embedded in malware to allow the compromised machine to be used as a proxy in such cases.)
Alerting that requires manual response is nigh on useless as by the time someone has been paged about something the horse has already bolted.
Knowing what has been taken is also a huge burden. 3800 repos that people now have to think about and decide what the implications are. Having been through something like this in the past there are plenty of times people go "I know that repo, it's fine, we can ignore that one" only for it to contain something they don't realise could be important.
These kind of attacks are going to become increasingly common as they're proven to work well and the mitigations for them are HARD. It doesn't need to be targeted at all either, you just infect a bunch of different things and see what gets sent in.
If companies continue to not pay the ransom then we're going to get a lot more things published and many companies having to apologise for all manner of things that end up being leaked.