It follows the naming convention TI used for its minicomputers of the era. The TI 990/4, /5, /9, /10, /10A, and /12 were all different models of the 990 series.

Exactly. There you have the principle used by TI at that time. As this is a microcomputer, not a mini, removing one zero, thus making this the TI 99 instead of the TI 990, makes sense.

Then the different models in the TI 990 series had different numbers, indicating their capacity. The TI 990/9 was the original model. The TI 990/4 and TI 990/5 had the TMS 9900 CPU inside. The model 5 just had some more memory.

Thus making the new home computer the TI 99/4 made sense. Later there were smaller models (e.g. the TI 99/2) and larger models (e.g. TI 99/8) planned and developed.

Adding the A to the type designation is just what TI did when they made a revision of something with about the same capability. The TI 990/10 and the TI 990/10A are both at roughly the same level, but the TI 990/10A was modernized with a new set of chips, based on the TMS 99105 CPU.

On a similar level, the TI 99/4 and the TI 99/4A are of similar capacity, or at least equal enough not to motivate a model name change to TI 99/5. So they added the A, as they always did, and came up with the TI 99/4A. It would have been the same even if the TMS 9918A chip would have been called TMS 99182 instead, or whatever.