LEP is the "Lifetime Expansion Pass" which could be purchased at various times between the Kickstarter and the release of the Horizons expansion, and gives you all "expansions" for free for the lifetime of the game, including access to their Alpha/Beta tests and pre-order bonuses. So far there have been two things counting as expansions - Horizons and Odyssey.
I don't think releasing the new ships via the Arx store rather than as an "ED Ships 2024" expansion was specifically intended to make them "not count as an expansion" [1] - the number of LEPs sold was never large enough to matter financially in that respect - but it has been a consequence of it which of course hasn't been entirely popular. (LEP holders, as any other Odyssey owner, do get access after the Arx-exclusive period ends)
[1] Most likely I think the reason for doing it that way was to avoid having to pay Steam 30% of the price on what they always expected to be a relatively small number of actual purchases.