So, from what I understand, the "deep" URL tracking in Adobe (the one you can only access with Raw Data feeds) will split the URL into multiple parts if it exceeds the character limit.
The custom dimensions we have access to, the max character count is 255... but in theory, you could try setting up "URL" and "URL (part 2)", and even "URL (part 3)" if your URLs are super long...
So if your URL is under 255 characters, just pass into URL.
If it's over, pass the first 255 into URL, then take the remainder and pass into URL (part 2)
If you need to potentially do a 3 part dimension, then you would apply the same logic to the "part 2" as you did on the main, checking for character count over 255 and splitting.
Now, using in Report Builder can be a bit tricky.. yes, you can add additional dimension columns... but in my experience, it loses the reference when you edit the request.. so it's something you have to be mindful of, but I am sure with some tweaking you should be able to make something work?
I would try to use a QA or Dev suite first, pass in a few pieces of sample data and make sure you can get it working before implementing a full solution.