Assume the reference antenna data is specified only in far field. Same data can then not be used in near field => system can not be calibrated.
All antennas have less directive gain in near field compared to far field and it is very complex to measure near field gain as radiating wave not is plane and antenna polarization is almost chaotic for both reference and measured antenna.
Distance of far field region is also depending on size of antenna aperture. High antenna gain for measured antenna increases size of near field region. Assume a parabolic antenna, 1 meter dia. and 10 GHz. 10*lambda is then 300mm but at that distance is it not any planar wave. In this case starts far field region maybe at 1000*lambda away. It is min distance to get reliable gain measurements.
It is not totally impossible to measure near field to get far field data. An example of exception is a stargate that measure at relative short distance and then with aid of very complex calculations can describe antenna far field behavior.
https://www.cst.com/Applications/Ar...ing-And-Measurement-Of-Wideband-Horn-Antennas
It requires a special type of anechoic chamber and is an expensive system. Advantage is that it is a fast method as it measure a complete circle for each position instead of rotating a slow turntable.
Antenna efficiency, in opposite to gain, can be measured with good result in near field but measurement tools must then be calibrated for near field use.
Anechoic chamber are problematic to use for near field as its anechoic properties only are valid for planar waves in a specific place inside chamber (quite zone).
Among working methods are Wheeler cap. It is a relative simple method:
https://www.rfcafe.com/references/articles/Efficiency-Measurement-Antenna-Wheeler-Cap.htm
Measurement in an echoic reverberation chamber is rather popular as it is a fast method.
https://www.bluetest.se have developed methods and hardware. Main idea is to rotate/reflect all waves inside a box with reflecting walls and measure an average sum of resulting fields.
Alternatively to an anechoic chamber can far field gain measurements be done at an empty parking lot with aid of an gated VNA (gated to avoid ground reflections). Even if there are a lot of surrounding man-made RF noise outdoor is probably result better then using near field measurement to find far field properties.