Regardless of how the rope trick spell is cast, a portal to the Astral Plane will not appear when a Bag of Holding enters the extradimensional space
The Bag of Holding states:
Placing a bag of holding inside an extradimensional space created by a Handy Haversack, Portable Hole, or similar item instantly destroys both items and opens a gate to the Astral Plane...
First off, we already know that a normal rope trick room would not create a portal to the Astral Plane because the room is not an item, nor was it created by an item.
What happens when the extradimensional space is created by an item (in this case a spell scroll) is perhaps uncertain, but there are two pieces of evidence that this would have the same results:
The Bag of Holding requires that the other plane be created by a similar item. I would not say that a spell scroll is similar to a Bag of Holding in the same way that Portable Holes and Handy Haversacks are. The latter two effectively are extradimensional spaces while a spell scroll certainly is not.
The Bag of Holding says that both items are destroyed, however in this case the spell scroll has already been destroyed, so this is somewhat unusual.
If we said the scroll does get destroyed then extending this situation to other items creates problems. For example: A Ring of Spell Storing. The ring would be destroyed, no matter the distance between it and the extradimensional space. Not only is destroying a magic item incredibly powerful, but where would the portal appear?
It does not matter how rope trick is cast; a portal to the Astral Plane would not appear because the item casting the spell is not similar to a Bag of Holding to the same degree that a Portable Hole and a Handy Haversack are.