Second completely independent and disposable WordPress installation in subdirectory?

Since your questions are quite vast and not completely WordPress related, I will stick to your main question.

The answer is: Yes. As long as you have it in different directories and don’t use the same prefix for their database tables or have a separate database for each (which means you can stuff more than one WP installation into one database with ease) you should be good to go.

As with either your main or your second WordPress installation, once you delete all folders/files and the database tables, your WordPress is being wiped, no matter what directory it is in.

I have a testing server with about 6-8 different WordPress instances, each for a different project with different plugins, themes, settings etc., all connected to one database. Only problem I ever had was with one installation using WPML and having messed up permalinks of another site, so that’s the only thing possibly interfering to my knowledge.

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