Yes, this is a native capability of HDL Coder. Each subsystem has a HDL Block property named "FlattenHierarchy" that can be either 'on', 'off', or 'auto'. The default value is 'auto'. which means that each subsystem will inherit its FlattenHierarchy setting from its parent. To completely flatten your entire design into a single flat HDL file, set 'FlattenHierarchy' to 'on' on your top-level subsystem. A more targeted approach is also possible, where you can mark specific sub-hierarchies for flattening (or not flattening) as you desire.
To access this property, you can use the hdlset_param command, or you can use the right-click context menu on a subsystem. Choose HDL Code>HDL Block Properties...>Flatten Hierarchy.