Why should pupbld.sql be run as SYSTEM (and not as SYS)?
The script creates certain objects, and it will put them in the current schema. Oracle wishes that these objects be created on SYSTEM schema, hence the requirement.

There are two Oracle schemas, SYS and SYSTEM, because they have two purposes. In short, SYS truly is the "special" user in respect to database internals, while SYSTEM works normally.

The SYS is the owner of the database, the only user with access to X$ tables, the only user which acts as SYSDBA (internally), that bypasses logon triggers, and that, for some obscure reason, cannot obtain read-consistent view of data. As a schema it holds crucial Oracle stuff, mainly the data dictionary.

The SYSTEM is fairly normal schema with DBA privilege (database administrator, not the same as SYSDBA), only that it is built-in and contains some additional (but also quite important) Oracle stuff. You shouldn't put your own stuff in this schema, if not instructed so by Oracle.