The method of converting codes is very generalized one, suppose in your design you have certain blocks; you characterize them as time sensitive, area sensitive etc, probably sensitive is not proper word, but what I actually mean is that one part of your system you want it to provide better timing and other to be area efficient, so using your Digital System Design techniques you will be able to code it in HDL accordingly but auto-converter (like MATLAB) won't cater for that so the reason is hardware utilization and efficient implementation, for efficient hardware utilization you would like to code it yourself and try to minimize resource utilization to the extent you want. So my opinion is that if someone is not good in HDL programming than this is good choice to utilize but for someone familiar with HDL prefer coding yourself.
Hope this helps, if not would like to discuss it further because it will help all of us to understand it better.