Hi Ilya,
I think i understand what you are trying to achieve. In general it is not recommended and very dangerous to modify the database of a Mendix app using other tools that Mendix itself. For Mendix to properly work, it need full control of the database schema. Adding a column in another way than via the domain model is very likely to lead to data loss in the future.
What is the reason not to add the boolean to the relevant entity via the domain model?