Is being featured on the front cover of a scientific journal an academic milestone?

Yes, it is a plus, and yes, you can add it to your CV. But it is (and should be) just one thing among many. It, alone, won't get you a job or a promotion, but it adds to the list of things that are positive about your contributions. The academic value will be positive, but small.

The paper is more important, of course. The image might induce a few more people to read your paper; a good thing.

Congratulations.

But your sense that you want to be known for the quality of your papers is the right attitude.

Several reputable journals I am familiar with ask authors to submit cover images. Once they receive the cover images, they ask the authors to pay a fee for the image to appear on the cover.

For people who know about this process, awareness that the authors may have paid a fee to appear on the cover decreases the prestige of appearing on the cover. People who do not know will be impressed.