This error message sounds strange. But what you try (thousands of exclusion areas) is out of spec at the moment and not really tested.
Instead I recommend you change the access after the import via the Java API directly.
I think if I modify the PBF by including the points or polygons, they would not be accessible when planning routes with GH, right?
You would need to modify existing ways (depending on the polygons) and add (access) tags based on which vehicles it should affect.
Another way could be to modify the access tags via the low level Java API (location index to find the edges to change the encoded values)