In Delphi's "Tools" menu there's a menu item called "madExcept configuration...". Clicking on that menu item opens a configuration dialog which lets you specify how you would like madExcept to behave inside of the Delphi IDE. Here's a screen shot of the configuration window:

The first and most important thing you can decide is whether you want madExcept to catch exceptions which happen inside of the Delphi IDE. Those exceptions can be bugs in the IDE or misbehaving third party packages. Or maybe your own component package.

In the section "what may madExcept do to your project?" you can specify what parts of your project madExcept may adjust to fit its own needs. E.g. when allowing changes in the compiler & linker options, madExcept makes sure that a detailed map file is generated.

Of course you can turn all that off. In that case madExcept doesn't hamper around with your project, anymore. However, it's your own responsibility then to make sure that madExcept gets what it needs to work correctly.