The open command cannot be used until the tables it uses exist and have entries for the table that is to be opened. (These minimum tables are pg_class, pg_attribute, pg_proc, and pg_type.) To allow those tables themselves to be filled, create with the bootstrap option implicitly opens the created table for data insertion.
Also, the declare index and declare toast commands cannot be used until the system catalogs they need have been created and filled in.
Thus, the structure of the postgres.bki file has to be:
create bootstrap one of the critical tables
insert data describing at least the critical tables
close
Repeat for the other critical tables.
create (without bootstrap) a noncritical table
open
insert desired data
close
Repeat for the other noncritical tables.
Define indexes and toast tables.
build indices
There are doubtless other, undocumented ordering dependencies.
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