OK, so on further testing of an in place upgrade of 5.5 to 5.6, it seems that there are system tables that are reporting as TABLE_CATEGORY_USER, specifically, the mysql.user table. Creating a regular end-user table is also of this type. So on running mysql_upgrade with some printing of interesting info from within check_engine() I get lots of errors (many trimmed for brevity):
**** check_engine    db_name[mysql]    table_name[user]    category[2]    no_substitution[0]    enf_engine[1]
InnoDB: Error: trying to create a MySQL system table mysql/user of type InnoDB.
InnoDB: MySQL system tables must be of the MyISAM type!
**** check_engine    db_name[mysql]    table_name[db]    category[2]    no_substitution[0]    enf_engine[1]
InnoDB: Error: trying to create a MySQL system table mysql/db of type InnoDB.
InnoDB: MySQL system tables must be of the MyISAM type!

Then eventually a server crash:
mysqld-debug: /home/glorch/dev/bug1218664/5.6/Percona-Server/sql/sql_error.cc:430: void Diagnostics_area::set_ok_status(ulonglong, ulonglong, const char*): Assertion `! is_set()' failed.
18:14:09 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed, 
something is definitely wrong and this may fail.
Please help us make Percona Server better by reporting any
bugs at http://bugs.percona.com/

key_buffer_size=8388608
read_buffer_size=131072
max_used_connections=1
max_threads=153
thread_count=1
connection_count=1
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 69137 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x3c6e4b0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 7f0e74456de0 thread_stack 0x40000
/data/bin/bug1218664/5.6/bin/mysqld-debug(my_print_stacktrace+0x35)[0xabc4ec]
/data/bin/bug1218664/5.6/bin/mysqld-debug(handle_fatal_signal+0x42e)[0x7316b6]
/lib64/libpthread.so.0[0x391b00f500]
/lib64/libc.so.6(gsignal+0x35)[0x391a8328a5]
/lib64/libc.so.6(abort+0x175)[0x391a834085]
/lib64/libc.so.6[0x391a82ba1e]
/lib64/libc.so.6(__assert_perror_fail+0x0)[0x391a82bae0]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_ZN16Diagnostics_area13set_ok_statusEyyPKc+0x66)[0x7afcde]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z5my_okP3THDyyPKc+0x4f)[0x7692c0]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z17mysql_alter_tableP3THDPcS1_P24st_ha_create_informationP10TABLE_LISTP10Alter_infojP8st_orderb+0x2606)[0x85ea4f]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_ZN19Sql_cmd_alter_table7executeEP3THD+0x51e)[0x9a95e4]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z21mysql_execute_commandP3THD+0x7e26)[0x7eba9e]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z11mysql_parseP3THDPcjP12Parser_state+0x58a)[0x7eed42]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z16dispatch_command19enum_server_commandP3THDPcj+0xd04)[0x7e14c4]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z10do_commandP3THD+0x3ae)[0x7e0385]
/data/bin/bug1218664/5.6/bin/mysqld-debug(_Z24do_handle_one_connectionP3THD+0x1cc)[0x7a7c74]
/data/bin/bug1218664/5.6/bin/mysqld-debug(handle_one_connection+0x33)[0x7a7742]
/data/bin/bug1218664/5.6/bin/mysqld-debug(pfs_spawn_thread+0x159)[0xdad33f]
/lib64/libpthread.so.0[0x391b007851]
/lib64/libc.so.6(clone+0x6d)[0x391a8e811d]


So I am now not sure what to do. I think at a minimum we need to document in our upgrade process that you MUST disable enforce-storage-engine during mysql_upgrade. Interestingly enough, if you enable it before initially creating your db and calling mysql_install_db you will also get a bunch of failures .