Well, I guess there's still the problem of how they get through the node if the portal is supposed to be inactive.
You could say that the node is stable enough that very small craft can traverse it in small numbers. Upon finding the node, the Apocalypse
sends an Anubis or Isis through to scout... and then the node suddenly stabilizes, as the scout finds the portal and accidentally activates it. This also helps makes the crew look "competent and forward-thinking".
Retail implies that the Ancients and Vasudans had peaceful contact in their history, and if you want to, you could even tie this into that. If the portal's subspace signature resembles that of a Vasudan jump drive, then the debrief could speculate that the scout's transit is what caused the node to reactivate. That answers the "no Shivans" question nicely - they could
send a fighter or two through, and maybe have in the past, but there's no benefit to doing so, so they don't any more.