I restored an Eternal Portal whose base Eternal Runed Flavolite block is at y=56 in the End and which generated an island on the ocean in the Overworld with the base block at y=62. I can pass from the Overworld to the End just fine. When passing from the End to the Overworld, though, I often (but not always) take half a heart of damage. (That's with all armor, status effects, etc., removed.) There are no obstructions in the immediate area on either side of the portal.

I'm playing on a server running the Valhelsia 3 modpack, version 3.4.1, with Minecraft 1.16.5 and BetterEndForge 1.6.0. I have operator privileges and log access; there is nothing output to the log from these teleports, not even a "moved wrongly".

(As an aside, I'm enjoying the biomes so much that I'm building my MineColonies colony in the End, atop a giant Mossy Glowshroom with custom schematics I've made to use your materials.)

An update: For unrelated reasons, I covered one side of each portal in the pair with solid blocks to force everyone through the other side only. (By "cover", I mean that each End Portal block now has a corresponding solid block XZ-adjacent to it, just outside of the frame.) This seems to have worked around the damage issue, as no damage is occurring at all now. I am also noticing a smoother visual when exiting the portal on the Overworld side; in retrospect, there was a bit of a visual jump on arrival before.