One thing you can be sure of is that you won't come up with a solution which everyone likes - but I think your suggestions look great. Unlike @sid, I like your idea for comments; as I mentioned in another feature request, I think comments are currently very awkward to use - to enter or to read.
I certainly agree that the borders help make things much clearer. However, some related problems - eg:
.. is perhaps as much a problem with Wappler's shortcomings as UI problems. In particular, the lack of an 'else if' condition potentially results in unnecessarily clumsy, difficult to read 'code'.