Would it be possible to move the world portal's surface so it aligns with the edge of the blocks, rather than the center (so for example with nether portals, you wouldn't see the obsidian at all), and then make it so the portal blocks are actually proxies to the other side's blocks ?
My idea is to build a large nether portal (say 5 by 5 or more), and then build train tracks, pipes and power cables, etc, THROUGH the portal. (Instead of using tesseracts and whatnot, i feel like this would be awesome)
(Similar : #44 , my idea is how you could implement it :) )

I see multiple issues with this:

1. Having no obsidian frame inside the portal looks wrong, as if something's broken
2. There is no generic way to make a "proxy block". While one can make a proxy block which works with most systems which use Forge's Capability API (certain pipes and cables), having it proxy to a different dimension seems very brittle and e.g. redstone and rails don't even use Forge's Capability API, neither do most high-performance pipe/cable systems.
3. A single portal has two sides but only one inner block. So if you put a rail on both sides, the inner block would now have to proxy to two different blocks on the remote portal. (again, Forge's Capability API allows for side-aware things but not everything is using it.)

1. Personally I like making my portals flush with the wall, so that you don't see the outer obsidian anyway.
   So I wouldn't mind not seeing the inner frame. Would feel like Portal's portals. (Maybe a thin glowing outline ?)
2. You don't really need proxies for rails, as long as they're straight, they can continue forward. For regular redstone, you can just make a portal block emit redstone on the same strength it receives on the other world. And for the other features, i'm fine if this uses forge capability API and some features don't work, that'd make me ask the other mods' authors to add capabilities to their mod, and everyone's happy.
3. How about enabling all of this only if the portal is closed off on one side ? (Adding more blocks of the same type as the frame to completely wall off one side of the portal, obsidian for the nether portal, teleporter frames for mekanism, etc ...)
   Obvisouly portals like twiligt forest and the end are already "one sided" portals (or at least i hope they are, wouldn't make sense to go into the end portal from below)
   That way you wouldn't have the mirroring problem.
   Thanks for your interest in my suggestions, i hope these clarifications will help you implement something interesting :)