Considering the PLL noise is much higher than the low phase noise amplifier, what is the typical application scenario for this category of amplifiers?

The most popular RF use case for a low phase noise amp in the LO chain is to boost up the input power to the LO port of the Mixer if the output power of the PLL+VCO circuit isn’t high enough for the minimum input power required on the LO port of the Mixer. For digital clocking applications, there is a use case for the gaining up the DAC output to improve the spectrum analyzers dynamic range.