I'm using the following id-generator in 5.0.0.CR1:
@Id()
@TableGenerator(name = "id_generator", allocationSize = 50)
@GeneratedValue(strategy = GenerationType.TABLE, generator = "id_generator")

The following SQL including setting a primary key is then generated:
create table hibernate_sequences (sequence_name varchar(255), sequence_next_hi_value bigint, primary key (sequence_name))

DB2 then returns an error due to using a nullable column as primary key:
HHH000389: Unsuccessful: create table hibernate_sequences (sequence_name varchar(255), sequence_next_hi_value bigint, primary key (sequence_name))
org.hibernate.tool.hbm2ddl.SchemaExport - DB2 SQL Error: SQLCODE=-542, SQLSTATE=42831, SQLERRMC=SEQUENCE_NAME, DRIVER=4.14.88

Testing with 4.3.10.Final no primary key setting is generated:
org.hibernate.SQL - create table L3PERF.hibernate_sequences ( sequence_name varchar(255), sequence_next_hi_value integer )
org.hibernate.tool.hbm2ddl.SchemaExport - HHH000230: Schema export complete