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Why extra hit points at 1st level: to increase 1st-level survivability.
Why vary these extra HP based on ancestry: flavour.
Also, the hit points aren't going to become irrelevant in just a level or two unless you are a high Con barbarian. If you have, for example, a Con 14 human cleric, your racial HP is slightly less than 10% of your total HP even at level 8. Level 8 is also the cut-off point where +2 Con gives you the same HP for a human.
If you mean that the difference between the ancestry hit points (a spread of 4 points) becomes irrelevant, that is pretty much true for all ancestry-related parts of a character: the different visions don't matter if you can get a magic item that replicates them, magical flight becomes available so your speed doesn't really matter (even less so if you're a monk since your bonus to speed eclipses the base speed, much less the differences between the ancestries), and you get way more ability boosts from level than you get from ancestry.