One typically gets packages from the distro's repository. And traffic with modern repositories uses HTTPS. So third parties don't see what packages are being used. And unless one configures a developer repository, there's never any traffic to the developer.
Also, IP addresses are considered PII under GDPR.
Edit: Still, if one cares that much about ones IP address, it's prudent to use a VPN service or Tor.
IP addresses are only PII if attached to other information. I can generate a list of IP addresses and store/sell that data and it's all fine because its meaningless without associated data.
In this case it would not be PII data if it was just an IP address in a webserver log saying someone checked for an update. It would be PII data if it was linked to your GitHub account.