The program does not “weave” any of your custom CSS into the exported bootstrap.min.css file. That file is never changed by the program. It’s simply overridden on the website by the CSS that comes after it. I cannot speak for what happens when you use the program’s built-in hosting, because I have my own web server where I host my sites, but when you export your BSS website project, it creates a folder called assets, with subfolders. The bootstrap subfolder contains the stock bootstrap.min.css. Another subfolder called css contains all your custom css files. The CSS files in this folder will take precedence over the stock bootstrap.min.css (and I believe this is the case whether you use the CDN bootstrap CSS, or the one generated by the program.)
If you are hosting your own sites, you have full control/freedom to modify/replace/delete any of the exported CSS files to your liking. If you want a version of bootstrap.min.css that doesn’t contain a particular part of the Bootstrap Framework, you can create a custom version here
And then replace the file that Bootstrap Studio generates and puts in the assets > bootstrap > css folder.
If you look at the source code of any page generated by BSS, you will see that the first linked CSS file is bootstrap.min.css. All your custom CSS comes after it, so if you wanted to, you could download bootstrap.min.css, import into BSS using the CSS import feature, and then edit it however you like using BSS’s editor, or a third party editor like Notepad++. You can also choose the include order of your custom CSS files by going to the Design panel (lower right) and right-clicking on “Styles” and select “include order” from the dropdown menu, to determine which of your custom files has the “final say” as it were.