This is to do with the shaders that AppGameKit uses internally. When an object is animated using bones (GetObjectNumBones>0), AppGameKit uses a specific shader to animate the object (using quaternions)
In ALL the other shaders, the agk_World matrix translates position and applies the scale to an object too. In the bone animated shader, agk_World is not applied at all
Just try using SetObjectScale() and not even that works on a bone animated object - so its not just tweens (No scale of any sort works due to the lack of agk_World being applied)
So...if you write a custom shader which is basically the standard bone animated one but with an additional application of scale values.... then you CAN actually scale an animated model too. If you reintroduce the agk_World variable and multiply the position then the model animates and the scale is applied but the translation gets applied twice so you have to remove the bottom row of the matrix in the shader. I've also tried this with a tween and it works with the tween scale too and SetObjectScale() works again correctly.
There is then potentially an issue of normals needing normalising in the shader too due to this potentially, but I wont go into that here. The point is that its to do with the animated shader and it is fixable by changing the shader if it is absolutely needed.
It probably wants raising as a bug on github and it is fixable fairly easily.
...The OP's issue is nothing to do with bone names. Depending on the model file format bone names can be loaded. Its just a case of it being dependent on the exact software used to produce the model. I've a few MS3D models where the bone names are loaded correctly. Seems to be quite flaky as do the animation names which dont seem to work with every filetype either.