I am doing it in two ways:
-The optional features in the regular classes are added automatically.
-Subclasses: So I've thought out it and like it this way. The Subclasses are kept as is. However, UA changes,missing features, and nerfs, that were applied to them in the actual publishing, can be regained/ for the subclass.
So for example, the UA Creation Bard: It's Dancing Item had an ability known as Endless Waltz, which allowed it to take Dodge, as a Bonus Action, after attacking. It was removed from the Published version of the Creation Bard's Dancing Item. Now if the published version of the PC Creation Bard can find a Higher Ranked Creation Bard NPC for training and fulfill the requirement for training, then the published version Creation Bard PC's Dancing Item regains the Endless Waltz feature from the UA Creation Bard article.
Or another Example: The Circle of Stars Druid. A very high leveled Circle of Stars Druid can undergo training to learn the UA Circle of Stars UA Capstone, Solar Flare. The Published version of the Circle of Stars Druid lost the Solar Flare from the UA version.
Like I said: they just don't added back in like that. Training must be done and discovered to do so.