Yeah, no problem. Making the portal accessible would kind of break the flow in that part of the game.
The bonus scene takes place right after returning to 1005 since Crono says "It's the first chance we've really had to sit down and talk". I guess what I'll do is this:
* At North Cape, the textbox asks you if you want to use the Time Egg or a different item.
* If you use the Time Egg, there's a warning, like "Are you sure? It's the last Time Egg we'll have in a while" or something.
* The other item you can use is the Annihilation Energy Agitator. It isn't powerful enough to open the distortion, but the fact that you can try to use it might make the player realize something is going on.
* If you complete all the sidequests, Belthasar will note that your Annihilation Energy Agitator has absorbed lots of...annihilation energy, recently, and that it can actually open the DBT distortion now. If you already used the Time Egg, he will add "You could have kept the Time Egg for a later use, ohoho!" or something. The characters could even repeat that sentence at North Cape, to make it really clear that the player could have kept the Time Egg.