Sudo commands created in the past have the sudocmd in their RDN, while the new case-sensitive ones have ipaUniqueID. In order for permissions to apply to both of these, use a targetfilter for objectclass=ipasudocmd instead of sudocmd=* in the target.
The update files are sorted before being processed because there are cases where order matters (such as getting schema added first, creating parent entries, etc). 10 - 20: Schema 20 - 30: FDS Configuration, new indices 30 - 40: Structual elements of the DIT 40 - 50: Pre-loaded data