Regarding your update:

I suppose it does not really matter if the source looks neat but I feel that the way the source looks represents how I code.

Bear in mind: the "source" that really matters is your perl code. Proper indenting makes a big difference there, and human readability is a high priority. Another important quality factor is "parsimony" -- avoidance of unnecessary work. If you add a significant amount of effort, code, cpu cycles, etc, to "solve" things that aren't really problems and that have no practical impact on the task at hand, the people who end up having to read your code may tend to have doubts about its value. (And you should be hoping that someday someone else will have to read your perl code.)

As for the html markup, I said before, when it works, it's unlikely that any human ever really looks at it, and those who do should know better than to have high expectations about indenting and so forth. We have HTML parsers to get around the unavoidable ugliness of it all.