Maybe they meant for Custom Lineage to also work more like Custom Subrace or Variant Race?
If that was the intent, then I would be fine with someone playing a Variant Elf or whatever. After all, compare Human to Variant Human:
Instead of gaining another 4 ASI +1s, you gain a Skill and a Feat. But, Variant Humans are still Humans.
A Variant Elf would give up Darkvision (maybe), Keen Senses, Fey Ancestry, Trance, and Elvish for a Feat and choice of Darkvision or a Skill.
I think WotC could have made the intent clearer by calling this Variant Lineage instead of Custom, and included that you can use the process as well to create a new race as well?