When you mention portals as holdings what comes to mind for me is the unharness portal that naturally occurs. Harnessing a portal like making a stargate or fading suns like gate around the portal to keep it there, power it, and use it on a more permanent basis would be required before it would be a holding. Or something like that. The gorgon’s alliance PC game implies that the neolithic structures of Stonehenge are sources, which could be used as a concept to justify gates or structures to focus and harness energies for the things in question.
Trade routes simply need a route and the traffic to travel that route unimpeded so I think anything is possible regarding Spelljammer trade routes, however I’d think it may be harder to blockade or decree them out of existence as borders are more easily circumvented. So that could be considered when making rules for them.
Again regarding portals I’d suggest a possible shadow taint from the nature of the Shadow world that can allow porting to have a risk of ending up trapped in the shadow world or something to that effect. Just a thought.
Ley lines going through portals? I’d require a focus or holding structure for them on the otherside of the portal. It may take more to maintain such a ley line and maybe even so much so that it’s best to keep them as a temporary thing. If you allow domain rules for other planes, then you can have sources and ley lines on the other side as well. Either way though there are just some ideas that come to mind that tend to be Cerilia centric. There is no need to increase or limit ley lines at all if you want this campaign and the domain rules to spread across the multiverse.
The physics of extra-planar terrain has always been fuzzy to me. Applying the domain rules to them should be easy by following the exceptions that have been made in adventures where structures and terrain has been layed out where PCs can function as the 3D creatures they are. (4D if you watch cosmos) Regarding trade routes I’d simply use a planar tag with each type of terrain so when you have forrests or mountains they’d be considered different from Cerilian forrests or mountains or other planar tagged types of parallel terrain. That is to say if water plane mountains were linked to fire plane or Cerilian mountains it’d be considered a different terrain type. Then again that’s just using earth physics for these planes, which I’ve found TSR…oops I mean WOTC doing with adventures and settings in outter planes settings.
Regarding your choice of rules being 3.5 I agree that is a much better choice than 4.
The limit on portals I would suggest being for harnessed portals on the holding level if you like the idea of what I had above. It seems the ideas are taking off here.