SKSE and Wabbajack

Sorry if this is a noob question but couldn’t find an existing answer for this specifically. I have already Skyrim SE with MO2 and SKSE. Say I wanted to install a wabbajack modlist on the same drive:

1. Would this automatically create a new portable instance of MO2 separate from my existing one (as long as I separate folders)?

2. Would the version of SKSE (or any other tools eg bodyslide, pandora, ssedit) which wabbajack installs automatically cause any issues with those same existing tools in the already existing MO2 instance?

Tldr; will wabbajack mods fuck up my existing game via the tools even though mod lists are separated?