One wordpress vs multiple performance

Hi everybody.
I have a wordpress website with many plugins and custom post types and functions.php with many custom filters and actions.
Assume that I want to add a new functionality to my website, for example a member area with reports, forms and other stuffs.
Now my question is this. If I can separate the the new section and run it on a new clean wordpress installation and just use the necessary plugins instead of integrating it with my existing wordpress site, does it influence on the performance or not.
I think that even though I don’t need the plugins and functions that are for my main website when seeing the member are, they all run and process each time I load the member are. And vice versa.
So If I have
– Section A with heavy coding and plugins with just 10 views a day
and
– Section B with light coding and no plugin with 10/000 views a day
even though it’s not needed, the section plugins and code run each time I load section B of the website.
Is that correct ?

I don’t know if I could describe the situation well.