I got an aswer from Joomlart Forums. I asked

Problem z-index

Hi, I had a problem in communitybuilder which uses jquery 1.5. It uses datetimepicker, but with your z-index in ja-container: 3 the datetimepicker was behind the ja-container. So I changed to z-index:5. Does this have somewhere bad consequences?

The answer is:

You can do it. It's a good way.

@pepperstreet:
I think it's better to take basic joomla templates as rules. And then to find solutions in the templates who changes something.

@jojo12
I know what you mean. As always, It really depends...
Just wanted to get a permanent solution, which applies to almost any new user, who wants to use GJ. If any user is responsible for the correct display... the GJ forum will be flooded with the same issues and questions (in the long-run). So, Kyle might be interested in such a solution as well

I agree, the joomlart Z-index usage in the inner template container is a bit strange. But most template will use different Z-indexes in different contexts and parts... so, a solution on GJ-side is preferred. If possible! (might be difficult, because Z-index behaviour changes in different CSS-specs and browsers ) The usual play with web-standards.