Here's the current clarification on Container Targets, in its entirety.
Container Targets
Spells with "container" Targets, including Circle, Room, Structure, and Boundary, can work in one of two ways.
First, they can affect any valid target within the Target container at the time of casting, and continue to affect those targets even if they leave the original Target area, for as long as the spell lasts. It does not affect anything that enters the Target container later, even if the spell is still in effect.
Second, they can affect any valid target within the Target container during the spell's period of effect. In this case, a valid target that leaves the container ceases to be affected by the spell, and a valid target that enters (or re-enters) the container is affected, until it leaves or the spell expires.
The way that a particular spell works is fixed when it is designed, and cannot be changed by the casting magus, although a spell working in one way is similar to a spell that is identical apart from working in the other, and so knowledge of one gives a bonus to inventing the other.
For example, a spell to put pink dots on people's foreheads with Target: Room and Duration: Moon could work in two ways. In the version that works in the first way, everyone in the room (on whom the spell Penetrates) at the time of casting gets a pink dot on their forehead, and this pink dot remains on their forehead until the new moon and full moon have both set. In the version that works in the second way, anyone who is inside the room (on whom the spell Penetrates) until the new moon and full moon have both set gets a pink dot on their forehead, even if they were not in the room when the spell was cast. When they leave the room, the pink dot disappears, although it reappears if they go back into the room. These two versions are two different spells, and a maga who wants to cast both (and cannot reliably cast them spontaneously) needs to create two spells.
A container may cease to exist as a container before the spell duration ends. If the spell is of the second type, the spell ends when the container ceases to exist. If it is of the first type, the spell is unaffected, unless the Target is Circle, in which case it ends when the circle is broken. A container can change to some extent without being destroyed. Opening a door to a room does not mean that the Room has been destroyed, while removing one of the walls completely normally would, as would adding a new wall to split the room into two rooms. On the other hand, a Structure would not cease to exist just because an interior room was split in two. Removing one wall of a room to make a larger room would normally destroy the Room, but adding a room to the top of a tower probably does not destroy the Structure. If a tent forms a room, then striking the tent and packing it away destroys the Room, but the walls can flex in the wind without the Room ceasing to exist. If the spell is initially cast with the tent partially folded, and then it is stretched out, the Room would normally get larger. The absolute limit to the growth of a container target is the size modifier of the spell. (Circles, again, are a special case, as they are defined by the circle traced at the time of casting, and cannot grow or shrink. Any attempt to do so would normally break the circle and end the spell.)
Most containers do not normally move, but they can. A Structure, for example, can be a ship. This is irrelevant to spells of the first type, which affect anything within the container at the time of casting, no matter what happens after that. Spells of the second type move with the container. Note that if a tower is magically ripped from the side of a keep and flown through the air, the rooms within the tower move with the tower, and Room-Target spells of the second type move with them, but the Structure has been destroyed, so any Structure Target spells of the second type end. Circles can move, but only if carried by the surface on which they are drawn. Boundaries are, by their nature, immobile. Any attempt to move a Boundary destroys it for magical purposes. (Note that, in Mythic Europe, the earth neither spins nor moves through space: things that do not move relative to the earth do not move at all.)
Circles and Rings in Three Dimensions
The standard Ars Magica rules use an intuitive definition of "inside the circle" for Circle Targets and Ring Durations. A person standing in the centre of a 1 pace diameter circle is inside the circle; someone who happens to be standing directly above it three floors higher is not. If your troupe need something more precise, you can work something out, and it should not break anything in the rules. Bear in mind, however, that it will still come down to the troupe's decision on whether a thing is within the more precisely defined volume.
Similar considerations apply to other container Targets if they are not closed in three dimensions, which is likely to be case for many Boundaries, and may be the case for Rooms or Structures.