You can tracking pixels to track per-user engagement. You can also use tracking links to connect the email address to website activity. As you say, it's possible to use these to track in the aggregate, but many platforms allow tracking by individual.
You are correct that the email was already personal data. But, GDPR requires that each new use of data be transparently communicated and legally justified (which may or may not mean consent), even if it's only using data you already have. The fact that they have already identified the user does not resolve the issue--GDPR still cares when you collect more data about a known user.
Meaning, even though you are justified using the email address to send the newsletter, you may not be in the clear building an engagement profile associated with that email. Which, apparently, some email marketers do.
Do they? Remember that under the GDPR, a five-page ToS with a "I consent" button at the end is not considered valid. In particular, the user must consent for each use of the PI separately. I don't remember ever seeing a specific consent box for building an engagement profile.
I would argue that pixel trackers for the purpose of checking whether the email is read is covered by the consent to receive marketing by email in the same way as what emails were sent to whom and when will likely also be tracked.
None of these are personal data if not liked to the email address, which they do not have to.
If linked to email address and considered personal data then the argument is what is covered by consent to receive email marketing? IMHO tracking whether the email was opened is covered (in the same way as agreeing to receive phone marketing should imply they can track whether you answered the phone...). They will also obviously keep track of what emails they sent you and when.
Now, what additional personal data are collected by tracking pixels?
> these are used to uniquely identify individuals
I would say that this isn't the case. It is to check that the email was read.