Just various notes, and answered questions.
You won't see it in the kernel APIs directly, however, bones are sent as commands in display lists (which are kicked off with sceGeListEnqueue). Games use GE_CMD_BONEMATRIXNUMBER / GE_CMD_BONEMATRIXDATA repeatedly to upload bone matrices into registers, then if the vertex format contains bone weights, skinning is applied accordingly.
Note that it's a fixed matrix palette of 8 matrices, so if you need more (and you almost always do) you need to split the model into multiple draws, and upload new matrices in between. Modern skinning instead has, for example, 4 weights and 4 matrix indices in each vertex, so each vertex can make use of up to four out of a large number of matrices.