Rely on the geolocation arrays and GDAL warp:
gdalwarp -te -5500000 -5500000 5500000 5500000 -t_srs "+proj=geos +lon_0=140.7 +h=35785863 +x_0=0 +y_0=0 +a=6378137 +b=6356752.3 +units=m +no_defs" vrt://AHI-CHGT_v1r1_h09_s202403040030204_e202403040039398_c202403040047497.nc?sd_name=CldTopTemp test.vrt
or, assign the grid and ignore the geolocation arrays (in this case we also need GDAL_NETCDF_BOTTOMUP=NO
)
"vrt://AHI-CHGT_v1r1_h09_s202403040030204_e202403040039398_c202403040047497.nc?sd_name=CldTopTemp&a_srs=+proj=geos +lon_0=140.7 +h=35785863 +x_0=0 +y_0=0 +a=6378137 +b=6356752.3 +units=m +no_defs&a_ullr=-5500000,5500000,5500000,-55000000"
file is at
https://noaa-himawari9.s3.amazonaws.com/AHI-L2-FLDK-Clouds/2024/03/04/0030/AHI-CHGT_v1r1_h09_s202403040030204_e202403040039398_c202403040047497.nc