Gpt and GDAL throws an error

Windows 7, x64, ENG.

When running gpt from the command line, it throws an error about the specified GDAL could not be found, although all the files are where the message says they aren’t.
The problem was noticed in an earlier thread for the beta version of SNAP 6, which however seems to be closed for additional replies now. GPT gdal dll load error

I guess this is due to my separate GDAL installation is prioritized over the internal GDAL, when running gpt from the command line, which is probably used in the Desktop version of SNAP.
How could this be fixed? Does it need to be fixed? Could this influence performance? gpt runs despite the error, however, it is performing way worse than the Desktop version, despite I have increased tile size, memory settings and so on.