Bill,
In some cases one would use a tuner between the rig and the amp if the input of the amp was, for some reason, not a 50 ohm load. This was not much of a problem with exciters using final tubes and pi network coupling but it bacame a problem with solid state exciters that had foldback SWR protection. The tuner then allowed the solid state exciter to "see" a 50 ohm load and delivered full power into it.
Another reason for this is that a tuner in the line cuts down on any harmonic radiation getting to the amplifier. There may be other reasons but these were the two I have heard of.
73
George
W3GEO