This, to me, is an interesting topic, but exactly why air bubbles form, by chance or by design, can really only be discussed through something like a full article with plenty of photos - many of which would need to be macro closeups and from a variety of angles.
However, a few comments here may generate further thought by others which could help to explain things one way or another.
In the links that you and Wuff have given to Richard More's weights with these types of cane, I cannot tell whether what we are seeing are actually air bubbles.
In some cases, I see possible air bubbles over what looks like a very thin pale purple rod, perhaps even with a white core. The structure of many rods around a central cane design is well known, and each rod can have its own surround of clear glass as well as there being clear glass around the central section of the cane. And a cane made up of several elements may also have a final surround of clear glass, sometimes with a fairly substantial amount.
If I am correct, then the purple rod may have had a "defect" of some form which is replicated in every cane slice and which then produces a bubble over its end. This would form a very neat ring of bubbles spaced evenly to match the number of rod canes in the outer ring. Hence the uniformity that is seen.
... when the canes are placed in the glass of the dome would the glass maker plan for the bubbles in their spacing of the cane in the closepack?
Even if bubbles were a planned part of a cane, it is simply the whole of the cane, including any clear glass surround that has been added which determines how it will look within the finished weights.
For closepack weights their very nature (having closely packed canes) means that no "spacing" of canes is planned. A suitable mix of canes is set out on a small metal plate, with all the canes set as close to each other as possible. Any cane with a clear glass surround will naturally form an apparent space between its neighbours. A gather of clear glass is pressed down onto the setup to pick all the canes up in one go. Sometimes this will cause canes to move, but the glass of the gather will fill any space created. After some initial shaping, the main dome of clear glass is added.
And yes, minute indents, cracks and so forth, however they are created in a cane, can give rise to what seems to be a "fairly large" air bubble. We see the cane though its clear dome - which acts as a magnifier, and any air bubble with its globular shape will appear larger than it actually is.Wuff's PP15 cane
The example cane that Wuff has shown from his PP15 weight, clearly does have uniformly set air bubbles. But without a detailed description of that cane, I cannot adequately comment on how the bubbles have formed. If there is no "rod" or similar element beneath each bubble, then I would be looking for a "defect" of some type.