I don't think this needs any fixes in the server. mysql_install_db can disable enforce-storage-engine from the server's command line.
Okay, if enforce-storage-engine cannot be disabled, then it's a bug on itself that needs fixing, but that should be done anyway, unrelated to bootstrap. So, to sum it up, there should be two changes:
- fix mysql_install_db to disable enforce-storage-engine from the server's command line.
- (optionally) fix the server to allow enforce-storage-engine to be disabled.
It should be disabled either with --enforce-storage-engine="" or --disable-enforce-storage-engine or, may be, both should work.
http://lists.askmonty.org/pipermail/commits/2015-August/008240.html