Enterprise customers are allowed to have multiple scripts mapped to different URL routes. This is mainly so that different teams owning different parts of the site don't step on each other. However, generally if you stuff your logic into one script rather than multiple, it will perform better, since that one script is more likely to be "hot" when needed.
Keep in mind that you can write your code as a bunch of modules and then use a tool like webpack to bundle it into one script, before you upload it to Cloudflare.
> for testing/development purposes
I agree with this, we definitely plan to add better ways to test script changes. Currently there is the online preview that shows next to the code editor, but it's true that there are some limits to what you can test with it.