Since you are wanting to run some custom CSS 3D transformations client side, I do not see any reason as to why this would not be possible.
What would want to do is add in a HTML element on your bubble page and add in any CSS 3D transforms, divs etc to that element.
A much more elegant way to do the above would be to use (or make) a Bubble plugin.
First I exported my HTML, CSS, and JS files from CodePen. Then, I uploaded these files to a free hosting site (i used 000webhost). Lastly, I executed the html page on there and copy/pasted the URL to a HTML element on my bubble page. I made the HTML element an iFrame.
This resulted in being able to use CSS3d in Bubble.is
Thanks for the feedback! Just to tell you, you can upload files on your Bubble app, because those free hosting options are very unreliable, especially 000webhost which is a shell to a shell that is a shell to another corporation and has very bad security practices that lead into user email and pasword leak.
Plus an iFrame is a very heavy and insecure method to use.