Oni said so himself. Because, as mentioned, he seems to have no idea what the numbers mean save that they are new versions.
On that vein,
That is not how numbering works, but at least you are not releasing something on version 0.999e so...
The first number is the release number. 0 means it is still in the works. 1 means it is complete. 2 means that it vent through a complete overhaul.
Thus why this being version 1.0 should mean it is complete.
The second number is for major aditions. In this game, it would seem to be 999, but it is more that Oni just shoved three numbers together instead without any .s as dividers.
For example, a visual novel or a story-based game would mean a chunk of the main story was added, and a more mechanics-oriented game would mean a new mechanic was added or majorly improved.
The third number would be a minor story addition, a side-story, minor extra mechanics, etc.
A fourth one is not that common, but it is the same thing - a lower level of improvements, not enough to increase the number before but still an addition.
And at the end a letter for bugfixes.
Thus how you can have something like a 0.6.8.2b, or 0.8.2.2.
Notice the .s, they allow you to have something like 0.3.10 instead of the limitation Oni is being forced into of needing to add another number after it reaches a 9. The current version would be something like 0.9.9.9e... as it is, pretty sure it would be closer to 0.14.12e or something.