Create module with custom entity and CRUD
The main purpose of content types/entity bundles is to allow users to configure/create subtypes/bundles of your entity type and add configurable fields to them.

If you want to have two different things, just create two different entity types. Each will have its own table then and its own set of fields. Completely separated.

If you want to have a single entity type/table with different sets of additional fields, then you can for example use entity bundles and just don't expose a UI for them, buy removing all forms, routes and the field_ui_base_route. Then the only way to add per-bundle fields would be through the API/Code.

Or you implement it all yourself using bundleFieldDefinitions(), hook_entity_field_storage_info() and so on. But that would require quite a bit of code as you need to take care of installing the field storage definitions and so on.