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I can't reproduce the error with HSQLDB 2.3.2 either. Could you post the exact error message that you get / the screeshots with the error message?
What is the version of HSQLDB you are using? I cannot reproduce the problem, neither with constraint name "id", nor "id_pk".

As for 2, you can define primary key as
Id bigint GENERATED ALWAYS AS IDENTITY PRIMARY KEY
but Vertabelo is prepared to handle multi-column primary keys. This is why it generates primary key as constraint.
We've talked about it here in the team. For now, it's not on our roadmap. I will keep the thread open so that other users can upvote or comment about this feature.
You have to check the checkbox "Generate comments for database objects" in the SQL generation settings. See the screenshot. Make sure the focus is not on any tables to see the Model properties panel.



I'm sorry I forgot to write about it in my previous answer.
The "Quote all identifies" checkbox now works for TABLESPACE and SCHEMA.
The validation is now available in Vertabelo.
Table and column descriptions are now generated as comments for table/column
Data Dictionary management is now available in Vertabelo.
I understand that you want the colors to be added automatically? There's no such feature in Vertabelo. We're thinking about adding some sort of view which would show a table and highlight the tables it is referencing. But it's an idea of a feature rather than a real planned feature yet. Would this sort of view meet your needs?

As of now, you can manually change the color of tables and reference lines in the Format section for each table/reference. 

If your diagrams are getting larger, you can use the Subject Area feature to organize the diagram. Here is a short feature overview video: https://www.youtube.com/watch?v=a79nEA0FN1M