Funny you mention joining and such...

When I UV'd and charted the model in Wings3D (I still model meshes in Wings, it's faster for me), I had different pieces joined in order to share the same maps for multiple parts. But separated everthing again afterwards. That way all the textures for adjacent parts can use a common map as their UV coords from the mapping process are retained. Keep in mind each part being separate makes mechanical models work easier for rigging, etc. (Something also seen a lot with game models.)

But regardless of how they're mapped, I still wish there were a way to paint textures on multiple parts by some group selection in Blender. (Without any need to join meshes.) Such a thing would definitely save time and improve workflow.

For now, texturing in a separate file with all the parts joined does seem to be the fastest way. Since the UV coordinates are the same for the model in both files, the texturing and resultant imagemap done on the one with joined parts will work just fine on the other where the parts remain separate. (More process to get stuff done, but ideally it shouldn't be necessary.)

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Barbequed Pixels?

Your friendly neighborhood Wings3D nut.
Also feel free to browse my freebies at ShareCG.
There might be something worth downloading.