I want to disallow a certain func_physbox to pass through portals. Is that possible? the physbox cannot be made larger, because up from a certain height the player can't pick it up anymore, no matter how low the mass scale is.

A filter should do that.
Create it and put the name of the physbox in it and set the option to disallow. Parent a func_clip_physics to both portals using a prop_portal and write the name of the filter into the right field. From now on everything that has the same name as the func_physbox can't go trough the clip in front of the portals.

yeah, I had this idea already, but it's kind of a strange workaround. If there is no better option, I guess I'll do it.

But shouldn't the filter be set to "allow all entities that match criteria", so that the clip works only for the physbox?

Now that you mention it..., I don't know. Try it out .

Parenting to portals works strangely, but SetOrigin works from a script.