Question

Can we add PHP scripts in our WordPress site in order to add an online tool in our blog?

Answer 1

Yes we can BUT BETTER

edit the funcions.php of current theme (if you do not going to update)

write plugins

create post types if are needed.

If you work without the Process and Logic of WordPress then better frozen the site (not allow updates), use a good plugin of security like WordFence, and to have often backups.