I would recommend using the current stable release (v1.0.20250506)
  https://github.com/rordenlab/dcm2niix/re...

I am unsure what the question is - it seems like you are converting the images two different ways and getting diferent JSONs, but I do not know what the difference between the "direct" and "indirect" mode. I would convert the files like this:
 dcm2niix /path/to/DICOMs

Is there some other tool you are using? If so does the tool use the same version of dcm2niix (the JSON should report the version `"ConversionSoftwareVersion": "v1.0.20250505"`). 

dcm2niix should populate the fields of the DICOM, those these vary from a system running V (e.g. VE11) versus XA (e.g. after upgrade to XA30).  Note that the CSA headers are crucial for many sequence details, so enure that your PACS or anonymization scripts do not remove these from the DICOMs before dcm2niix converts them.

https://github.com/rordenlab/dcm2niix/tree/master/BIDS