Our main processor, xsltproc, is not a general-purpose compiler, and does not “call” external programs. That is the primary purpose of the mbx script. You will see a configuration file, script/mbx.cfg, as part of the distribution. Read the comments at the top of this file, but foremost, realize that you are not meant to edit this file. It is a template, and any changes you make will be overwritten with an original version when you update. Instead, make a copy and place it as mathbook/user/mbx.cfg. The script will look for this copy first, then fallback to the generic version.
The entries of this file are the names of executable files that perform certain tasks as part of the script's functions. If it seems that certain helper programs are not being found, you can provide full path names, and that may solve the problem.