Correct. Only one entry is allowed per school/organization/club with a multi-team program. To clarify, only ONE team submits the final entry for a multi-team program; all contributing teams decide which one team will submit. Multiple entries from the same program will be disqualified.
If the top prize is won by a multi-team program, only one team can qualify for VEX Worlds, as only one spot is available. It is up to the winning school/organization/club to decide which ONE team wins the qualification spot to VEX Worlds.