I just tested this with the remote debugger in PyCharm 2016.3.2 and it works like a charm.
Thanks for releasing this. Here are some steps that I followed to get remote debugger in PyCharm working alongside MXSPyCOM.
In PyCharm open Settings->Tools->External Tools.
Add a new item, which will open the Edit Tool window.
Fill out Name, Description fields, but most important is to point the Programs field to your MXSPyCom.exe, and in Parameters enter '-f $FilePath$' (without quotes).
PyCharm includes a remote debugging module called pydevd (located under PyCharm installation\helpers\pydevd). You need to initialize a trace from the python script so that the remote debugger can trap any exceptions or breakpoints.
Add the full path to pydevd to your PYTHONPATH or include it in your sys.path dynamically.
Once you successfully import pydevd, make sure to include the following at the beginning of your script code.
pydevd.settrace(host, port=7720, suspend=False)
Last but not least, create a new Python Remoted Debug configuration, and call it whatever you want. Change the port settings to those you set in pydevd.settrace (7720) and run the remote debugger before sending your script to 3dsMax using the MXSPyCom.exe external tool.