Okay, so end portals themselves are 2d. This means if you stand on level with them, they are invisible. I noticed this while trying to see how I could trap an end portal, and wanted to try it out on an SMP, but the server has spigot/paper. The mushroom bug to break end portal frames likely does not work.
Whether you use an ender pearl or not makes zero difference. All the game is detecting is that your hitbox collides with the portal block, it doesn’t care how you get there. Ender pearl, swim, crawl, fly, etc. They’re all processed the same.
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