By nature, the GPL causes everything to be changed to be under the GPL
license. If you have 1000 pieces of code that are licensed under MIT for
example and someone puts in 1 GPL code, the entire codebase becomes copyleft
whether you wanted to or not.
Speaking of the custom plugins that are not copyleft and are included with
copyleft code that is not dual licensed causes the custom plugins to now fall
under the GPL. Maybe you never wanted the source code for those plugins to
become free software because they were never meant to be and fit a specific
purpose that the client paid for. Too late... the GPL converted them whether
you like it or not and now your code can be stolen and shared.
You don't care about the core application due to it being free software to
begin with and you want it to be. The plugins which are given to the client
after they paid for them as a download are not and must be kept protected.
You want everything to be free and in the wild and I am saying there are case
scenarios when you don't want it to be.