I probe, so I'mma try to answer this, since no one else has.
A smaller diameter probe has a greater chance of puncturing the 'out pocket' of a female, her hemipenal homologue, than does a larger probe. This is because it's easier to concentrate too much pressure on the smaller point than on the larger if the prober doesn't really know what they're doing. That's the big risk of not knowing how to probe. Then, if a pocket was punctured in the past, it's easier to re-enter the remaining hole with a smaller probe than with a larger one. From what I understand, once punctured, the puncture is there for the life of the snake.
On the flip side, some of the weird depths might be natural. BPs in general seem more flexible about probing depths than, say, corn snakes. Because it's relatively common for too-small probes to go very deep in female pythons, I'm not sure that the full pocket isn't sometimes fairly long, it's just that it narrows so quickly, an appropriately sized probe usually won't go past 3-4 scales on most girls. *
What did the breeder you brought this female to for probing say she was, male or female? Did he talk you through it at all?
*The occasional female will go deeper, just to confuse things.
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