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We analyzed this a few months ago and decided not to do. The main problem is related to foreign key naming convention. Every database architect may have own naming convention, so it hard to follow it. 
Thanks for your suggestions. We rethink how to do it better.
It works as described in yours suggestion. When nullable is checked and you check the PK the nullable field is unchecked automatically. 

Did you encounter situation that both nullable and PK were checked at the same time?

We''ve just fixed it. It will be on production with the nearest upgrade - I mean next week.

Thanks.
We would like to keep Vertabelo UI for basic elements simple, so we don't plan to extend it in such cases. 

But you can add such index to the model using table "Additional SQL scripts" tab as you can see on picture below.

You are right. We will fix it asap. However this doesn't block generating SQL and uritype will appear in generated SQL code.

Thanks for reporting this.
In Vertabelo there is one diagram for one model. If you want to divide your models into separated areas "subject area" can help. I think you omit one important functionality related to subject areas. I mean "Shortcuts". Tables, Views and References may have many graphical representations on diagram. So you can have a table visible in two different subject areas that doesn't need to be close to each other.

Here is the short video tutorial about managing large diagrams in Vertabelo  https://www.youtube.com/watch?v=a79nEA0FN1M&list=P...

The design decision in this matter wasn't simple. It is a trade-off between full abstraction (parts of model + diagrams) and simplicity. In Vertabelo we generally stand up on simplicity, this way some features known from big desktop tools are not available.