Is very easy to export animated md5 models, to idtech 4 after you know how (obviously).
First you need to have a working md5 exporter for blender.
Second you need to know how to correctly use that exporter, the one i use for example (the one graciously given by the arx team), needs the exported bones to be in a separated layer, layer 5 to be exact. That is so you can have a complex animating rig in one layer and only export the bones you need in another.
Third the root bone MOST be called origin, is a requirement and it is used as the root point of the animated model, as well has the "floor" for characters, so it should be put where it makes sense, like between the feet of a character. Btw i don't know if this is really necessary but i heard that you should animate the root bone as well when you want a model to move from a place to another ingame.
Four you need to make a .def file for the animated model, is a requirement, in this .def file you define, the md5 mesh and the md5 animations, this file is very important and very powerful, on it you can define from particle effects to particular sounds that come from particular bones or animation frames, plus other things.
Five a idle animation should always be defined, it can be a single frame.
About bone limitations, i'm no expert but this is what i recall, idtech 4 supports max 256 bones on a single character (the animation rig on blender or others can have more but it should be baked to 256 bones or less) and a vertex on the mesh can only be assigned to a single bone, but the bone can influence many vertex's (this is equal to many other engines), md5 only supports bone animation.