Change JPEG2000 to GeoTIFF inside product folder

Is possible to translate from jp2 to geotiff inside the Product without using S2Atoolbox? (Ej, using gdal_translate) But, in the way that S2Atoolbox would be able to read geotif instead jp2 from the Because, for massive processing purpose, we would like to change the format to geotiff but, conserving PRODUCT.SAFE structure in order to also some users could be able to use the S2Atoolbox and accessing the data in our storage system.
I translate all the jp2 files to geotiff and I also change the data format from JPEG2000 TO GeoTIFF in the xml file but, the s2atollbox gives NullPointerException when I am trying to open the product folder

These kind of product modifications are not supported. S2TBX only read products conforming to PSD.

Why would you want to change the format?

Because the code/decode time for JP2000 is higher than GeoTiff and, If we would like to compute global mask processing (I mean massive parallel processing) would improve the performance. In other hand, we would like to keep the structure in order to use also the S2Atbx.