I was just playing a College of Lore Bard at the end of early access and I am 99% sure I was able to make my own additional skill picks then.

I wanted to play essentially the same character on release but I was not able to to the additional skill picks anymore. In addition the Skill Expertise picks didn't show in the right hand selector. You had to see and use the "Skill" button in the main level up window
which is easy to miss once it scrolls offscreen. I'm also pretty sure that was correctly present in the last early access version I played.

On that skill selector it then also shows off the wrong/incomplete class skills I selected with the icons on the left of the skills to boot (though the tickboxes are still there correctly).

I had the same background (Urchin) and I'm pretty sure I would have noticed being hard locked to a duplicate of a skill I had already. Or did I fabulate that?

The skill picks are indeed hard coded to Athletics, Sleight of Hand, and Intimidation, and apparently this is a known issue, but the fix didn't make it into release. This is a big problem because if the skills overlap with your background, you simply lose out on the skill pick.

https://forums.larian.com/ubbthreads.php?ubb=showflat&Number=819081

The warlock's pact of the tome has a similar issue where you cannot pick the cantrips granted. We should refile these bug reports so that Larian reprioritizes these issues.