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I wouldn't expect it for free because you don't need to touch the clutch when you're replacing a transmission. The only thing related to the clutch is the throw-out bearing, which will need to be transferred over from the old transmission, or a new one installed.
He should charge you a minimal fee to replace the clutch, maybe a bit more if he opts to resurface the flywheel, even more so if he chooses to replace the flywheel. I wouldn't expect more than an hour of labour on top of the transmission replacement to re/re the pressure plate and clutch disk once the transmission is out.
That being said, you should have him look at replacing the RMS (rear main seal) and maybe even the IMS bearing since he will have done 80% of the work for those jobs in replace your clutch and transmission.
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