The Inter typeface is very versatile and has many different options and variants, including more distinguishable uppercase i and lowercase L. The article just installed the base version as an example. https://rsms.me/inter/
Like most modern fonts, it supports a lot of OpenType features, so this can be changed dynamically. Changing some settings by default has already been mentioned in the discussion around the change.
IIRC this issue is mentioned in the gitlab discussions (from months ago ... not sure how this became news suddenly); they're looking to patch Inter if they decide to use it as the UI font.
The article isn't great as it fails to mention that Gnome is considering a variation of Inter and not the default and therefore the article uses the wrong font in the screenshot. It addresses some of the concerns people have mentioned, like the capital I and lower l being the same
Cantarell has served us well, but we’ve been wondering if it would be more beneficial to default to a more modern and well-maintained typeface
Eh. I don't feel Cantarell "dated" or "not modern". I don't even use GNOME anymore but I reckon Cantarell is actually a great font, it's legible and has character. It's almost like you can tell it's about GNOME when you see Cantarell somewhere. If I were them I'd invest into giving it more weights (I'd really like it if it had a lighter version), variations and extending it. They have the power and resources to do so.
imho they're trying to solve a problem that doesn't even exist. Inter's default is a poor choice, as some of you have already noted here.