No, this toolchain is used by MCUXpresso IDE (and only by that version), as it is inside the IDE installation folder. So you can replace that one. But of course it will be that toolchain for all your projects you are using with that installation folder. If you still want to use another one (or the original one), you can install yet another instance of the IDE.
If you want to set the toolchain for each project: you can use the GNU MCU (now part of Eclipse CDT) plugins: GNU MCU → Eclipse Embedded CDT!