Yes and no … it really depends on the nature of the modification and / or the package that you have installed.
For example … I use a non-standard port for SSH. That modification remains untouched by MiaB. I also have Webmin installed. Again, no issues.
In older versions of MiaB (I do not know if this still exists, but have no reason to think otherwise) some of the .css and .js files for the admin pages loaded from an offsite server somewhere. My SysAdmin did not like that so he modified the pages so that they would load from local copies. Those had to be re-modified every time the config script was re-run.
So … it really depends …